3K6S: Integrin alphaXbeta2 ectodomain

Structure of integrin alphaXbeta2 ectodomain. Determined by X-ray diffraction at 3.5 Å resolution. Released 12 Jan 2010.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 50,187
Mol. weight: 796.01 kDa
Ligands: MAN, NAG, CA, MG
Released: 12 Jan 2010

Explore 3K6S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K6S contains 149 α-helices and 512 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 89 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-11	3	2
β-strand	21-24	4	3
β-strand	29-33	5	3
β-strand	47-51	5	3
β-strand	56-59	4	3
β-strand	76-80	5	4
β-strand	85-90	6	4
β-strand	94-95	2	5
β-strand	102-103	2	5
β-strand	106-110	5	4
β-strand	116	1	4
α-helix	125-129	5
β-strand	131-138	8	6
α-helix	146-160	15
β-strand	167-174	8	6
β-strand	178-182	5	6
α-helix	185-188	4
α-helix	193-196	4
β-strand	207	1	7
α-helix	209-217	9
β-strand	232-239	8	6
β-strand	244	1	7
α-helix	250-260	11
β-strand	262-264	3	6
β-strand	267-268	2	6
β-strand	269	1	8
α-helix	272-274	3
α-helix	280-283	4
α-helix	287	1
β-strand	297	1	8
α-helix	301-304	4
α-helix	310-315	6
β-strand	332	1	5
β-strand	339-340	2	9
β-strand	347-350	4	9
β-strand	358	1	10
β-strand	359-362	4	9
α-helix	368-369	2
β-strand	370-372	3	9
β-strand	386	1	10
β-strand	390-391	2	11
β-strand	400-405	6	11
α-helix	408-410	3
β-strand	413-418	6	11
β-strand	426-430	5	11
β-strand	443-446	4	12
β-strand	456-460	5	12
β-strand	471	1	13
β-strand	473-477	5	12
β-strand	502	1	13
β-strand	506-510	5	14
β-strand	519-523	5	14
β-strand	533	1	15
β-strand	534-538	5	14
β-strand	539	1	16
β-strand	545	1	16
β-strand	551	1	14
β-strand	554	1	15
β-strand	565-571	7	2
β-strand	582-587	6	2
β-strand	591-595	5	2
β-strand	596	1	1
β-strand	599	1	17
β-strand	602-608	7	18
β-strand	629-639	11	18
β-strand	654-662	9	19
β-strand	672-673	2	18
β-strand	680-687	8	19
β-strand	692-700	9	18
α-helix	710	1
β-strand	711-717	7	19
β-strand	733	1	17
β-strand	742-746	5	19
β-strand	764-767	4	20
β-strand	775-776	2	21
β-strand	781-788	8	20
α-helix	794	1
β-strand	795	1	22
β-strand	799-804	6	23
β-strand	808-811	4	20
β-strand	828-833	6	23
β-strand	840-845	6	23
β-strand	851	1	22
β-strand	857-865	9	20
β-strand	874-877	4	24
β-strand	878-882	5	23
β-strand	883	1	25
β-strand	886	1	25
β-strand	896-900	5	24
β-strand	902-905	4	21
β-strand	908-911	4	26
β-strand	932-939	8	26
β-strand	946-953	8	27
β-strand	964	1	28
β-strand	968-970	3	26
β-strand	979-984	6	27
α-helix	991-997	7
β-strand	1000-1001	2	27
β-strand	1008-1018	11	27
β-strand	1025-1030	6	26
β-strand	1032	1	28
α-helix	1035-1038	4
β-strand	1045-1054	10	27
β-strand	1060-1062	3	21
β-strand	1071-1078	8	27

Chain B: 28 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	22-24	3	29
α-helix	37-39	3
β-strand	40-41	2	29
α-helix	43-49	7
β-strand	56-57	2	29
β-strand	62	1	30
β-strand	65	1	31
β-strand	77	1	32
β-strand	81	1	31
β-strand	82-85	4	30
α-helix	86	1
β-strand	91-97	7	32
α-helix	102-105	4
β-strand	106-112	7	33
α-helix	118-122	5
α-helix	131-136	6
β-strand	143-149	7	33
α-helix	176-179	4
β-strand	183-189	7	33
α-helix	193-200	8
α-helix	214-221	8
α-helix	225-228	4
β-strand	236-240	5	33
α-helix	250-254	5
β-strand	270	1	33
α-helix	274-276	3
α-helix	278-281	4
α-helix	282-284	3
α-helix	285-291	7
β-strand	295	1	33
β-strand	298-300	3	34
α-helix	302-304	3
α-helix	305-314	10
β-strand	320-322	3	34
α-helix	331-333	3
α-helix	337-341	5
β-strand	349	1	35
β-strand	356-359	4	32
β-strand	362	1	36
β-strand	370	1	36
β-strand	387-395	9	32
α-helix	399-400	2
β-strand	402-405	4	30
β-strand	406	1	35
α-helix	407-408	2
β-strand	416-421	6	30
α-helix	437-439	3
β-strand	441-443	3	37
β-strand	448-450	3	37
β-strand	454-455	2	38
β-strand	461-462	2	38
α-helix	470-472	3
α-helix	483-485	3
β-strand	488-491	4	39
β-strand	494-497	4	39
β-strand	507-508	2	40
β-strand	514-515	2	40
β-strand	521-522	2	41
β-strand	525-526	2	41
α-helix	529-532	4
β-strand	533-536	4	42
β-strand	539-542	4	42
α-helix	543	1
β-strand	561	1	43
β-strand	567	1	43
β-strand	574	1	44
β-strand	579	1	44
α-helix	604-607	4
β-strand	629	1	45
β-strand	640-643	4	46
β-strand	649-654	6	46
β-strand	664	1	45
β-strand	665-667	3	46

Chain C: 7 helices, 81 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	47
β-strand	9-11	3	48
β-strand	21-24	4	49
β-strand	29-33	5	49
β-strand	47-51	5	49
β-strand	56-59	4	49
β-strand	76-80	5	50
β-strand	85-90	6	50
β-strand	94-95	2	51
β-strand	102-103	2	51
β-strand	106-110	5	50
β-strand	116	1	50
α-helix	125-127	3
β-strand	332	1	51
β-strand	339-340	2	52
β-strand	347-350	4	52
β-strand	358	1	53
β-strand	359-362	4	52
α-helix	368-369	2
β-strand	370-372	3	52
β-strand	386	1	53
β-strand	390-391	2	54
β-strand	400-405	6	54
α-helix	408-410	3
β-strand	413-418	6	54
β-strand	426-430	5	54
β-strand	443-446	4	55
β-strand	456-460	5	55
β-strand	471	1	56
β-strand	473-477	5	55
β-strand	502	1	56
β-strand	506-510	5	57
β-strand	519-523	5	57
β-strand	533	1	58
β-strand	534-538	5	57
β-strand	539	1	59
β-strand	545	1	59
β-strand	551	1	57
β-strand	554	1	58
β-strand	565-571	7	48
β-strand	582-587	6	48
β-strand	591-595	5	48
β-strand	596	1	47
β-strand	599	1	60
β-strand	602-608	7	61
β-strand	619	1	62
β-strand	629-639	11	61
β-strand	654-662	9	63
β-strand	672-673	2	61
β-strand	680-687	8	63
β-strand	692-700	9	61
β-strand	703	1	62
α-helix	710	1
β-strand	711-717	7	63
β-strand	733	1	60
β-strand	742-746	5	63
β-strand	764-767	4	64
β-strand	775-776	2	65
β-strand	781-788	8	64
α-helix	794	1
β-strand	795	1	66
β-strand	799-804	6	67
β-strand	808-811	4	64
β-strand	828-833	6	67
β-strand	840-845	6	67
β-strand	851	1	66
β-strand	857-865	9	64
β-strand	874-877	4	24
β-strand	878-882	5	67
β-strand	883	1	68
β-strand	886	1	68
β-strand	896-900	5	24
β-strand	902-905	4	65
β-strand	908-911	4	69
β-strand	932-939	8	69
β-strand	946-953	8	70
β-strand	964	1	71
β-strand	968-970	3	69
β-strand	979-984	6	70
α-helix	991-997	7
β-strand	1000-1001	2	70
β-strand	1008-1018	11	70
β-strand	1025-1030	6	69
β-strand	1032	1	71
α-helix	1035-1038	4
β-strand	1045-1054	10	70
β-strand	1060-1062	3	65
β-strand	1071-1078	8	70

Chain D: 28 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	22-24	3	72
α-helix	37-39	3
β-strand	40-41	2	72
α-helix	43-49	7
β-strand	56-57	2	72
β-strand	62	1	73
β-strand	65	1	74
β-strand	77	1	75
β-strand	81	1	74
β-strand	83-85	3	73
α-helix	86	1
β-strand	91-97	7	75
α-helix	103-105	3
β-strand	106-112	7	76
α-helix	118-122	5
α-helix	131-136	6
β-strand	143-149	7	76
α-helix	176-179	4
β-strand	183-189	7	76
α-helix	193-200	8
α-helix	214-221	8
α-helix	225-228	4
β-strand	236-240	5	76
α-helix	250-254	5
β-strand	270	1	76
α-helix	274-276	3
α-helix	278-281	4
α-helix	282-284	3
α-helix	285-291	7
β-strand	295	1	76
β-strand	298-300	3	77
α-helix	302-304	3
α-helix	305-314	10
β-strand	320-322	3	77
α-helix	331-333	3
α-helix	337-341	5
β-strand	349	1	78
β-strand	356-359	4	75
β-strand	362	1	79
β-strand	370	1	79
β-strand	387-395	9	75
α-helix	399-400	2
β-strand	402-405	4	73
β-strand	406	1	78
α-helix	407-408	2
β-strand	416-421	6	73
α-helix	437-439	3
β-strand	441-443	3	80
β-strand	448-450	3	80
β-strand	454-455	2	81
β-strand	461-462	2	81
α-helix	470-472	3
α-helix	483-485	3
β-strand	488-491	4	82
β-strand	494-497	4	82
β-strand	508	1	83
β-strand	514	1	83
β-strand	521-522	2	84
β-strand	525-526	2	84
α-helix	529-532	4
β-strand	533-536	4	85
β-strand	539-542	4	85
α-helix	543	1
β-strand	561	1	86
β-strand	567	1	86
β-strand	574	1	87
β-strand	579	1	87
α-helix	604-607	4
β-strand	629	1	88
β-strand	640-643	4	89
β-strand	649-654	6	89
β-strand	664	1	88
β-strand	665-667	3	89

Chains E and G: 7 helices, 79 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	90
β-strand	9-11	3	91
β-strand	21-24	4	92
β-strand	29-33	5	92
β-strand	47-51	5	92
β-strand	56-59	4	92
β-strand	76-80	5	93
β-strand	85-90	6	93
β-strand	94-95	2	94
β-strand	102-103	2	94
β-strand	106-110	5	93
β-strand	116	1	93
α-helix	125-127	3
β-strand	332	1	94
β-strand	339-340	2	95
β-strand	347-350	4	95
β-strand	358	1	96
β-strand	359-362	4	95
α-helix	368-369	2
β-strand	370-372	3	95
β-strand	386	1	96
β-strand	390-391	2	97
β-strand	400-405	6	97
α-helix	408-410	3
β-strand	413-418	6	97
β-strand	426-430	5	97
β-strand	443-446	4	98
β-strand	456-460	5	98
β-strand	471	1	99
β-strand	473-477	5	98
β-strand	502	1	99
β-strand	506-510	5	100
β-strand	519-523	5	100
β-strand	533	1	101
β-strand	534-538	5	100
β-strand	539	1	102
β-strand	545	1	102
β-strand	551	1	100
β-strand	554	1	101
β-strand	565-571	7	91
β-strand	582-587	6	91
β-strand	591-595	5	91
β-strand	596	1	90
β-strand	599	1	103
β-strand	602-608	7	104
β-strand	629-639	11	104
β-strand	654-662	9	105
β-strand	672-673	2	104
β-strand	680-687	8	105
β-strand	692-700	9	104
α-helix	710	1
β-strand	711-717	7	105
β-strand	733	1	103
β-strand	742-746	5	105
β-strand	764-767	4	106
β-strand	775-776	2	107
β-strand	781-788	8	106
α-helix	794	1
β-strand	795	1	108
β-strand	799-804	6	109
β-strand	808-811	4	106
β-strand	828-833	6	109
β-strand	840-845	6	109
β-strand	851	1	108
β-strand	857-865	9	106
β-strand	874-877	4	110
β-strand	878-882	5	109
β-strand	883	1	111
β-strand	886	1	111
β-strand	896-900	5	110
β-strand	902-905	4	107
β-strand	908-911	4	112
β-strand	932-939	8	112
β-strand	946-953	8	113
β-strand	964	1	114
β-strand	968-970	3	112
β-strand	979-984	6	113
α-helix	991-997	7
β-strand	1000-1001	2	113
β-strand	1008-1018	11	113
β-strand	1025-1030	6	112
β-strand	1032	1	114
α-helix	1035-1038	4
β-strand	1045-1054	10	113
β-strand	1060-1062	3	107
β-strand	1071-1078	8	113

Chain F: 28 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	22-24	3	115
α-helix	37-39	3
β-strand	40-41	2	115
α-helix	43-49	7
β-strand	56-57	2	115
β-strand	62	1	116
β-strand	65	1	117
β-strand	77	1	118
β-strand	81	1	117
β-strand	83-85	3	116
α-helix	86	1
β-strand	91-97	7	118
α-helix	102-105	4
β-strand	107-112	6	119
α-helix	118-122	5
α-helix	131-136	6
β-strand	144-149	6	119
α-helix	176-179	4
β-strand	183-189	7	119
α-helix	193-200	8
α-helix	214-221	8
α-helix	225-228	4
β-strand	236-240	5	119
α-helix	250-254	5
β-strand	270	1	119
α-helix	274-276	3
α-helix	278-281	4
α-helix	282-284	3
α-helix	285-291	7
β-strand	295	1	119
β-strand	298-300	3	120
α-helix	302-304	3
α-helix	305-314	10
β-strand	320-322	3	120
α-helix	331-333	3
α-helix	337-341	5
β-strand	349	1	121
β-strand	356-359	4	118
β-strand	362	1	122
β-strand	370	1	122
β-strand	387-395	9	118
α-helix	399-400	2
β-strand	402-405	4	116
β-strand	406	1	121
α-helix	407-408	2
β-strand	416-421	6	116
α-helix	437-439	3
β-strand	441-443	3	123
β-strand	448-450	3	123
β-strand	454-455	2	124
β-strand	461-462	2	124
α-helix	470-472	3
α-helix	483-485	3
β-strand	488-491	4	125
β-strand	494-497	4	125
β-strand	507-508	2	126
β-strand	514-515	2	126
β-strand	521-522	2	127
β-strand	525-526	2	127
α-helix	529-532	4
β-strand	533-536	4	128
β-strand	539-542	4	128
α-helix	543	1
β-strand	561	1	129
β-strand	567	1	129
β-strand	574	1	130
β-strand	579	1	130
α-helix	604-607	4
β-strand	629	1	131
β-strand	640-643	4	132
β-strand	649-654	6	132
β-strand	664	1	131
β-strand	665-667	3	132

Chain H: 27 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	22-24	3	157
α-helix	37-39	3
β-strand	40-41	2	157
α-helix	43-49	7
β-strand	56-57	2	157
β-strand	62	1	158
β-strand	65	1	159
β-strand	77	1	160
β-strand	81	1	159
β-strand	82-85	4	158
α-helix	86	1
β-strand	91-97	7	160
α-helix	103-105	3
β-strand	106-112	7	161
α-helix	118-122	5
α-helix	131-136	6
β-strand	143-149	7	161
α-helix	176-179	4
β-strand	183-189	7	161
α-helix	193-200	8
α-helix	214-221	8
α-helix	225-228	4
β-strand	236-240	5	161
α-helix	250-254	5
β-strand	270	1	161
α-helix	274-276	3
α-helix	278-281	4
α-helix	282-284	3
α-helix	285-291	7
β-strand	295	1	161
β-strand	298-300	3	162
α-helix	302-304	3
α-helix	305-314	10
β-strand	320-322	3	162
α-helix	331-333	3
α-helix	337-341	5
β-strand	349	1	163
β-strand	356-359	4	160
β-strand	362	1	164
β-strand	370	1	164
β-strand	387-395	9	160
α-helix	399-400	2
β-strand	402-405	4	158
β-strand	406	1	163
β-strand	416-421	6	158
α-helix	437-439	3
β-strand	441-443	3	165
β-strand	448-450	3	165
β-strand	454-455	2	166
β-strand	461-462	2	166
α-helix	470-472	3
α-helix	483-485	3
β-strand	488-491	4	167
β-strand	494-497	4	167
β-strand	507-508	2	168
β-strand	514-515	2	168
β-strand	521-522	2	169
β-strand	525-526	2	169
α-helix	529-532	4
β-strand	533-536	4	170
β-strand	539-542	4	170
α-helix	543	1
β-strand	561	1	171
β-strand	567	1	171
β-strand	574	1	172
β-strand	579	1	172
α-helix	604-607	4
β-strand	629	1	173
β-strand	640-643	4	174
β-strand	649-654	6	174
β-strand	664	1	173
β-strand	665-667	3	174

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-X	A, C, E, G	protein	1095	Homo sapiens	P20702 (AlphaFold model)
Integrin beta-2	B, D, F, H	protein	687	Homo sapiens	P05107 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3K6S_1 Integrin alpha-X (chains A, C, E, G)
FNLDTEELTAFRVDSAGFGDSVVQYANSWVVVGAPQKITAANQTGGLYQCGYSTGACEPI
GLQVPPEAVNMSLGLSLASTTSPSQLLACGPTVHHECGRNMYLTGLCFLLGPTQLTQRLP
VSRQECPRQEQDIVFLIDGSGSISSRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQT
HFTFEEFRRSSNPLSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITD
GKKEGDSLDYKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIASKPSQEHIFKVEDF
DALKDIQNQLKEKIFAIEGTETTSSSSFELEMAQEGFSAVFTPDGPVLGAVGSFTWSGGA
FLYPPNMSPTFINMSQENVDMRDSYLGYSTELALWKGVQSLVLGAPRYQHTGKAVIFTQV
SRQWRMKAEVTGTQIGSYFGASLCSVDVDSDGSTDLVLIGAPHYYEQTRGGQVSVCPLPR
GWRRWWCDAVLYGEQGHPWGRFGAALTVLGDVNGDKLTDVVIGAPGEEENRGAVYLFHGV
LGPSISPSHSQRIAGSQLSSRLQYFGQALSGGQDLTQDGLVDLAVGARGQVLLLRTRPVL
WVGVSMQFIPAEIPRSAFECREQVVSEQTLVQSNICLYIDKRSKNLLGSRDLQSSVTLDL
ALDPGRLSPRATFQETKNRSLSRVRVLGLKAHCENFNLLLPSCVEDSVTPITLRLNFTLV
GKPLLAFRNLRPMLAADAQRYFTASLPFEKNCGADHICQDNLGISFSFPGLKSLLVGSNL
ELNAEVMVWNDGEDSYGTTITFSHPAGLSYRYVAEGQKQGQLRSLHLTCDSAPVGSQGTW
STSCRINHLIFRGGAQITFLATFDVSPKAVLGDRLLLTANVSSENNTPRTSKTTFQLELP
VKYAVYTVVSSHEQFTKYLNFSESEEKESHVAMHRYQVNNLGQRDLPVSINFWVPVELNQ
EAVWMDVEVSHPQNPSLRCSSEKIAPPASDFLAHIQKNPVLDCSIAGCLRFRCDVPSFSV
QEELDFTLKGNLSFGWVRQILQKKVSVVSVAEITFDTSVYSQLPGQEAFMRAQTTTVLEK
YKVHGCGGLENLYFQ

Sequence of entity 2 (B, D, F, H), FASTA

>3K6S_2 Integrin beta-2 (chains B, D, F, H)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNN
SIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKC
RCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPC
GKYISCAECLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGM
DRYLIYVDESRECVAGPDGCGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12
CA	Calcium ion	Ca	16
MG	Magnesium ion	Mg	1

Primary citation

Structure of an integrin with an alphaI domain, complement receptor type 4. Xie, C., Zhu, J., Chen, X. et al. EMBO J (2010) 29:666-679. DOI 10.1038/emboj.2009.367 · PubMed

Other PDB entries of the same protein (UniProt P20702 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1N3Y 1.65 Å, Crystal structure of the alpha-X beta2 integrin I domain
4NEH 2.75 Å, An internal ligand-bound, metastable state of a leukocyte integrin, aXb2
4NEN 2.9 Å, An internal ligand-bound, metastable state of a leukocyte integrin, aXb2
5ES4 3.3 Å, Re-refinement of integrin ALPHAXBETA2 ectodomain in the closed/bent conformation
3K72 3.7 Å, Structure of integrin alphaX beta2
3K71 3.95 Å, Structure of integrin alphaX beta2 ectodomain
2LUV Structure and Binding Interface of the Cytosolic Tails of aXb2 Integrin
9ECM Structure of the human integrin alphaX transmembrane domain

Browse structure collections

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