5E6S: Integrin alpha-L

Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand. Determined by X-ray diffraction at 2.15 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 6
Atoms: 26,342
Mol. weight: 436.89 kDa
Ligands: NAG, CA, MG
Released: 2 Mar 2016

Explore 5E6S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E6S contains 133 α-helices and 222 β-strands across 6 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: 20 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-11	3	2
β-strand	23-27	5	3
β-strand	30-35	6	3
α-helix	36-38	3
α-helix	41-43	3
β-strand	44-48	5	3
β-strand	55-57	3	3
α-helix	58-60	3
β-strand	73-76	4	4
β-strand	83-94	12	4
β-strand	97-107	11	4
β-strand	115-118	4	4
β-strand	130-137	8	5
β-strand	139	1	6
α-helix	144-160	17
β-strand	166-173	8	5
β-strand	177-181	5	5
α-helix	183-189	7
α-helix	192-195	4
β-strand	204	1	6
α-helix	208-214	7
α-helix	215-219	5
α-helix	222-224	3
β-strand	231-238	8	5
α-helix	249-251	3
β-strand	255-261	7	5
α-helix	263-265	3
α-helix	268-272	5
α-helix	275-277	3
α-helix	282-285	4
β-strand	286-289	4	5
α-helix	292-298	7
α-helix	299-302	4
β-strand	327-334	8	7
β-strand	337-342	6	7
α-helix	345-348	4
β-strand	350	1	8
β-strand	351-355	5	7
β-strand	362-366	5	7
β-strand	379	1	8
β-strand	382-386	5	9
β-strand	388	1	10
α-helix	392-393	2
β-strand	394-399	6	9
α-helix	402-404	3
β-strand	407-412	6	9
β-strand	421-427	7	9
β-strand	438-442	5	11
β-strand	449	1	10
β-strand	452-457	6	11
β-strand	465	1	12
β-strand	468-474	7	11
β-strand	479-485	7	11
β-strand	491	1	12
β-strand	499-502	4	13
β-strand	514-518	5	13
β-strand	524	1	14
β-strand	525-529	5	13
β-strand	531-532	2	15
β-strand	535-536	2	15
β-strand	542-545	4	13
α-helix	546-549	4
β-strand	556	1	14
β-strand	559-564	6	2
β-strand	573-578	6	2
β-strand	581-586	6	2
β-strand	587	1	1

Chain B: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
β-strand	22-24	3	16
α-helix	36-39	4
β-strand	40-41	2	16
α-helix	43-48	6
α-helix	53-55	3
β-strand	56-57	2	16
β-strand	62-66	5	17
β-strand	76-77	2	18
β-strand	80-85	6	17
β-strand	91-97	7	18
α-helix	102-104	3
β-strand	105-112	8	19
α-helix	115-117	3
α-helix	118-124	7
α-helix	128-138	11
β-strand	143-149	7	19
α-helix	162-166	5
β-strand	176	1	20
β-strand	182-189	8	19
α-helix	192-200	9
β-strand	204	1	20
β-strand	212	1	21
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-241	8	19
β-strand	245	1	21
α-helix	250-254	5
α-helix	259-260	2
β-strand	266-267	2	19
β-strand	270-271	2	19
α-helix	272-275	4
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-300	7	19
α-helix	302-304	3
α-helix	305-309	5
α-helix	311-314	4
β-strand	319-322	4	19
α-helix	323-324	2
α-helix	330-342	13
β-strand	345-349	5	17
β-strand	356-363	8	18
β-strand	369-373	5	18
β-strand	376-378	3	17
β-strand	387-395	9	18
α-helix	399-400	2
β-strand	402-408	7	17
β-strand	414-421	8	17
α-helix	441	1
β-strand	442-444	3	22
β-strand	447-449	3	22
α-helix	450-451	2

Chain C: 23 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	23
β-strand	23-27	5	24
β-strand	30-35	6	24
α-helix	36-38	3
α-helix	41-43	3
β-strand	44-49	6	24
β-strand	55-57	3	24
α-helix	58-59	2
β-strand	73-76	4	25
β-strand	83-94	12	25
β-strand	97-107	11	25
β-strand	115-118	4	25
β-strand	130-137	8	26
β-strand	139	1	27
α-helix	144-160	17
β-strand	167-173	7	26
β-strand	177-181	5	26
α-helix	183-189	7
α-helix	192-195	4
β-strand	204	1	27
α-helix	208-218	11
α-helix	222-224	3
β-strand	231-238	8	26
α-helix	249-251	3
β-strand	255-261	7	26
α-helix	263-265	3
α-helix	268-272	5
α-helix	275-277	3
α-helix	279	1
α-helix	281	1
α-helix	282-285	4
β-strand	286-289	4	26
α-helix	292-294	3
α-helix	295-303	9
β-strand	327-334	8	28
β-strand	337-342	6	28
α-helix	345-348	4
β-strand	350	1	29
β-strand	351-355	5	28
β-strand	362-366	5	28
β-strand	379	1	29
β-strand	382-386	5	30
β-strand	388	1	31
α-helix	392-393	2
β-strand	394-399	6	30
α-helix	402-404	3
β-strand	407-412	6	30
α-helix	413-414	2
β-strand	421-427	7	30
β-strand	438-442	5	32
β-strand	449	1	31
β-strand	452-457	6	32
β-strand	465	1	33
β-strand	468-474	7	32
β-strand	479-484	6	32
α-helix	487-488	2
β-strand	491	1	33
β-strand	499-502	4	34
β-strand	514-518	5	34
β-strand	524	1	35
β-strand	525-529	5	34
β-strand	531-532	2	36
β-strand	535-536	2	36
β-strand	542-545	4	34
α-helix	546-549	4
β-strand	556	1	35
β-strand	559-561	3	23
β-strand	573-578	6	23
β-strand	581-587	7	23

Chain D: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	22-24	3	37
α-helix	36-39	4
β-strand	40-41	2	37
α-helix	43-48	6
α-helix	53-55	3
β-strand	56-57	2	37
β-strand	62-66	5	38
β-strand	76-77	2	39
β-strand	80-85	6	38
β-strand	86	1	40
β-strand	89	1	40
β-strand	91-97	7	39
β-strand	105-112	8	41
α-helix	115-117	3
α-helix	118-124	7
α-helix	128-138	11
β-strand	143-149	7	41
α-helix	162-166	5
β-strand	182-189	8	41
α-helix	192-200	9
β-strand	212	1	42
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-241	8	41
β-strand	245	1	42
α-helix	250-254	5
α-helix	259-260	2
β-strand	266-267	2	41
β-strand	270-271	2	41
α-helix	272-276	5
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-301	8	41
α-helix	302-304	3
α-helix	305-309	5
α-helix	311-314	4
β-strand	319-323	5	41
α-helix	324	1
α-helix	330-342	13
β-strand	345-349	5	38
β-strand	356-363	8	39
β-strand	369-373	5	39
β-strand	376-378	3	38
β-strand	387-395	9	39
α-helix	399-400	2
β-strand	402-408	7	38
β-strand	414-421	8	38
α-helix	441	1
β-strand	442-444	3	43
β-strand	447-449	3	43

Chain E: 17 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	44
α-helix	5-7	3
β-strand	9-11	3	45
β-strand	23-27	5	46
β-strand	30-35	6	46
α-helix	36-38	3
β-strand	44-49	6	46
β-strand	55-57	3	46
β-strand	73-76	4	47
β-strand	83-94	12	47
β-strand	97-107	11	47
β-strand	115-118	4	47
α-helix	122-125	4
β-strand	130-137	8	48
β-strand	139	1	49
α-helix	144-161	18
β-strand	166-173	8	48
β-strand	177-181	5	48
α-helix	183-189	7
α-helix	192-195	4
β-strand	204	1	49
α-helix	208-218	11
α-helix	222-224	3
β-strand	231-238	8	48
α-helix	249-251	3
β-strand	255-261	7	48
α-helix	263-265	3
α-helix	268-272	5
α-helix	282-285	4
β-strand	286-289	4	48
α-helix	294-297	4
β-strand	327-334	8	50
β-strand	337-342	6	50
α-helix	345-348	4
β-strand	350	1	51
β-strand	352-355	4	50
β-strand	362-365	4	50
β-strand	379	1	51
β-strand	382-386	5	52
β-strand	388	1	53
β-strand	394-399	6	52
α-helix	402-404	3
β-strand	407-412	6	52
β-strand	421-427	7	52
β-strand	438-442	5	54
β-strand	449	1	53
β-strand	452-457	6	54
β-strand	465	1	55
β-strand	468-474	7	54
β-strand	479-485	7	54
α-helix	486-488	3
β-strand	491	1	55
β-strand	499-502	4	56
β-strand	514-518	5	56
β-strand	525-529	5	56
β-strand	531-532	2	57
β-strand	535-536	2	57
β-strand	542-545	4	56
α-helix	546-549	4
β-strand	559-564	6	45
β-strand	573-578	6	45
β-strand	581-586	6	45
β-strand	587	1	44

Chain F: 25 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
β-strand	22-24	3	58
α-helix	36-39	4
β-strand	40-41	2	58
α-helix	43-48	6
α-helix	53-55	3
β-strand	56-57	2	58
β-strand	62-66	5	59
β-strand	76-77	2	60
β-strand	80-85	6	59
α-helix	86	1
β-strand	91-97	7	60
β-strand	105-112	8	61
α-helix	115-117	3
α-helix	118-124	7
α-helix	128-138	11
β-strand	142-149	8	61
α-helix	162-166	5
α-helix	177-179	3
β-strand	182-189	8	61
α-helix	192-200	9
β-strand	212	1	62
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-241	8	61
β-strand	245	1	62
α-helix	250-254	5
α-helix	259-260	2
β-strand	266-267	2	61
β-strand	270-271	2	61
α-helix	272-276	5
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-300	7	61
α-helix	302-304	3
α-helix	305-309	5
α-helix	310-313	4
β-strand	319-322	4	61
α-helix	323-324	2
α-helix	330-342	13
β-strand	345-349	5	59
β-strand	356-363	8	60
β-strand	369-373	5	60
β-strand	376-378	3	59
β-strand	387-395	9	60
α-helix	399-401	3
β-strand	402-408	7	59
β-strand	414-421	8	59
α-helix	441	1
β-strand	442-444	3	63
β-strand	447-449	3	63

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-L	A, C, E	protein	795	Homo sapiens	P20701 (AlphaFold model)
Integrin beta-2	B, D, F	protein	510	Homo sapiens	P05107 (AlphaFold model)

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

>5E6S_1 Integrin alpha-L (chains A, C, E)
YNLDVRGARSFSPPRAGRHFGYRVLQVGNGVIVGAPGEGNSTGSLYQCQSGTGHCLPVTL
RGSNYTSKYLGMTLATDPTDGSILACDPGLSRTCDQNTYLSGLCYLFRQNLQGPMLQGRP
GFQECIKGNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTE
FDFSDYVKWKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDG
EATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFT
ELQKKIYVIEGTSKQDLTSFNMELSSSGISADLSRGHAVVGAVGAKDWAGGFLDLKADLQ
DDTFIGNEPLTPEVRAGYLGYTVTWLPSRQKTSLLASGAPRYQHMGRVLLFQEPQGGGHW
SQVQTIHGTQIGSYFGGELCGVDVDQDGETELLLIGAPLFYGEQRGGRVFIYQRRQLGFE
EVSELQGDPGYPLGRFGEAITALTDINGDGLVDVAVGAPLEEQGAVYIFNGRHGGLSPQP
SQRIEGTQVLSGIQWFGRSIHGVKDLEGDGLADVAVGAESQMIVLSSRPVVDMVTLMSFS
PAEIPVHEVECSYSTSNKMKEGVNITICFQIKSLIPQFQGRLVARLTYTLQLDGHRTRRR
GLFPGGRHELRRNIAVTTSMSCTDFSFHFPVCVQDLISPIRVSLNFSLWEEEGTPRDQRA
QGKDIPPILRPSLHSETWEIPFEKNPAALQTLFQGPLGAQGEKELQALEKENAQLEWELQ
ALEKELAQHHHHHHA

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

>5E6S_2 Integrin beta-2 (chains B, D, F)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRKVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEPAALQTLFQGPLGAQGKKKL
QALKKKNAQLKWKLQALKKKLAQHHHHHHA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
CA	Calcium ion	Ca	15
MG	Magnesium ion	Mg	3

Primary citation

Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops. Sen, M., Springer, T.A. Proc Natl Acad Sci U S A (2016) 113:2940-2945. DOI 10.1073/pnas.1601379113 · PubMed

Other PDB entries of the same protein (UniProt P20701 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MJN 1.3 Å, Crystal Structure of the intermediate affinity aL I domain mutant
2ICA 1.56 Å, CD11a (LFA1) I-domain complexed with BMS-587101 aka 5-[(5S,…
3F78 1.6 Å, Crystal structure of wild type LFA1 I domain complexed with isoflurane
1T0P 1.66 Å, Structural Basis of ICAM recognition by integrin alpahLbeta2 revealed in the complex…
3F74 1.7 Å, Crystal structure of wild type LFA1 I domain
2O7N 1.75 Å, CD11A (LFA1) I-domain complexed with 7A-[(4-cyanophenyl)methyl]-6-(3,5-dichlorophenyl)-5-…
1LFA 1.8 Å, CD11A I-domain with bound MN++
1XUO 1.8 Å, X-ray structure of LFA-1 I-domain bound to a 1,4-diazepane-2,5-dione inhibitor at 1.8A…
3BQN 1.8 Å, LFA-1 I domain bound to inhibitors
4IXD 1.8 Å, X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a resolution
7KC3 1.8 Å, X-ray structure of Lfa-1 I domain collected at 273 K
3M6F 1.85 Å, CD11A I-domain complexed with 6-((5S,9R)-9-(4-CYANOPHENYL)-3-(3,5-DICHLOROPHENYL)-1-METHY…

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