3ZDY: Integrin alpha-iib

Integrin alphaIIB beta3 headpiece and RGD peptide complex. Determined by X-ray diffraction at 2.45 Å resolution. Released 5 Jun 2013.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: HOMO SAPIENS, MUS MUSCULUS
Chains: 10
Atoms: 22,086
Mol. weight: 303.82 kDa
Ligands: CA, NAG, MG
Released: 5 Jun 2013

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

Secondary structure: helices and β-sheets

3ZDY contains 86 α-helices and 247 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: 9 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	22-27	6	3
β-strand	33-39	7	3
β-strand	43	1	4
β-strand	49	1	4
β-strand	51	1	5
β-strand	52-57	6	3
α-helix	58	1
β-strand	63	1	2
β-strand	67	1	3
β-strand	76-79	4	6
β-strand	82-87	6	6
β-strand	93	1	5
β-strand	96-100	5	7
β-strand	103-108	6	7
β-strand	112-117	6	6
β-strand	120-121	2	6
β-strand	125	1	6
β-strand	128	1	8
β-strand	129-134	6	7
β-strand	139-143	5	7
α-helix	152-157	6
β-strand	169	1	8
β-strand	172-175	4	9
β-strand	180-185	6	9
α-helix	188-191	4
β-strand	194-199	6	9
α-helix	200-206	7
β-strand	214	1	10
β-strand	220-221	2	9
α-helix	228-230	3
β-strand	238-242	5	11
β-strand	252-257	6	11
α-helix	260-263	4
β-strand	266-270	5	11
β-strand	276-281	6	11
β-strand	292-296	5	12
β-strand	305-310	6	12
β-strand	314-317	4	13
β-strand	321-324	4	13
β-strand	327-331	5	12
α-helix	332-334	3
β-strand	345-348	4	12
β-strand	359-364	6	14
β-strand	373-378	6	14
β-strand	388-392	5	14
β-strand	394-395	2	15
β-strand	398-399	2	15
β-strand	405-408	4	14
β-strand	420-425	6	2
β-strand	434-439	6	2
α-helix	440-442	3
β-strand	444-448	5	2
α-helix	449	1
β-strand	450	1	1

Chain B: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	13-19	7
β-strand	23-26	4	16
β-strand	38-40	3	16
α-helix	41-45	5
β-strand	54-55	2	16
β-strand	60-65	6	17
α-helix	67-70	4
β-strand	72	1	18
β-strand	83-84	2	19
β-strand	87-92	6	17
β-strand	97-105	9	19
β-strand	108	1	18
β-strand	112-119	8	20
α-helix	122-124	3
α-helix	127-130	4
α-helix	134-142	9
β-strand	149-156	8	20
α-helix	171-174	4
α-helix	178-180	3
α-helix	185-187	3
β-strand	190-197	8	20
α-helix	201-209	9
β-strand	220	1	21
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	20
β-strand	254	1	21
α-helix	259-263	5
α-helix	267-269	3
β-strand	275	1	22
β-strand	280	1	20
β-strand	281	1	22
α-helix	288-291	4
α-helix	292-301	10
β-strand	305-311	7	20
α-helix	315-322	8
β-strand	329-333	5	20
α-helix	340-351	12
β-strand	355-356	2	23
β-strand	357-360	4	17
β-strand	366-374	9	19
β-strand	378-381	4	19
β-strand	385-386	2	23
β-strand	394-403	10	19
β-strand	411-418	8	17
β-strand	425-431	7	17
α-helix	436-440	5
β-strand	442	1	24
β-strand	453-456	4	24
β-strand	459-462	4	24
α-helix	463	1

Chain C: 11 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	25
β-strand	9-12	4	26
β-strand	22-27	6	27
β-strand	33-38	6	27
β-strand	43	1	28
β-strand	49	1	28
β-strand	51	1	29
β-strand	53-57	5	27
α-helix	58	1
β-strand	63	1	26
β-strand	67	1	27
β-strand	76-79	4	30
β-strand	82-87	6	30
β-strand	93	1	29
β-strand	96-100	5	31
β-strand	103-108	6	31
β-strand	112-117	6	30
β-strand	120-121	2	30
β-strand	125	1	30
β-strand	128	1	32
β-strand	129-134	6	31
β-strand	139-143	5	31
α-helix	152-157	6
β-strand	169	1	32
β-strand	172-175	4	33
β-strand	180-185	6	33
α-helix	188-191	4
β-strand	193	1	34
β-strand	194-199	6	33
α-helix	200-205	6
β-strand	214	1	35
β-strand	220-221	2	33
α-helix	228-230	3
β-strand	235	1	34
β-strand	238-242	5	36
β-strand	252-257	6	36
α-helix	260-263	4
β-strand	266-270	5	36
β-strand	276-281	6	36
β-strand	292-296	5	37
β-strand	305-310	6	37
α-helix	313	1
β-strand	314-317	4	38
β-strand	321-324	4	38
β-strand	327-331	5	37
α-helix	332-334	3
α-helix	338-340	3
β-strand	345-348	4	37
β-strand	359-364	6	39
β-strand	373-378	6	39
β-strand	388-392	5	39
β-strand	394-395	2	40
β-strand	398-399	2	40
β-strand	405-408	4	39
α-helix	412	1
β-strand	420-425	6	26
β-strand	434-439	6	26
α-helix	440-442	3
β-strand	444-448	5	26
β-strand	450	1	25

Chain D: 23 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	13-19	7
β-strand	24-26	3	41
β-strand	38-39	2	41
α-helix	41-46	6
α-helix	51-53	3
β-strand	54-55	2	41
β-strand	60-65	6	42
α-helix	67-70	4
β-strand	72	1	43
α-helix	77-79	3
β-strand	83-84	2	44
β-strand	87-92	6	42
β-strand	97-105	9	44
β-strand	108	1	43
β-strand	112-119	8	45
α-helix	122-124	3
α-helix	125-130	6
α-helix	134-142	9
β-strand	149-156	8	45
α-helix	170-174	5
α-helix	185-187	3
β-strand	190-197	8	45
α-helix	201-209	9
β-strand	220	1	46
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	45
β-strand	254	1	46
α-helix	260-263	4
α-helix	268-269	2
β-strand	275	1	47
β-strand	280	1	45
β-strand	281	1	47
α-helix	288-291	4
α-helix	292-302	11
β-strand	305-311	7	45
α-helix	312-314	3
α-helix	315-322	8
β-strand	329-333	5	45
α-helix	340-351	12
β-strand	355-356	2	48
β-strand	357-360	4	42
β-strand	366-373	8	44
β-strand	379-381	3	44
β-strand	385-386	2	48
β-strand	394-403	10	44
β-strand	411-418	8	42
β-strand	425-431	7	42
α-helix	436-440	5
β-strand	442	1	49
β-strand	453-456	4	49
β-strand	459-462	4	49
α-helix	463	1

Chain E: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	50
β-strand	10-12	3	51
β-strand	18-25	8	50
α-helix	29-31	3
β-strand	34-39	6	51
β-strand	45-51	7	51
β-strand	58-60	3	51
α-helix	62-64	3
β-strand	68-73	6	50
β-strand	78-83	6	50
α-helix	88-90	3
β-strand	92-98	7	51
β-strand	102	1	35
β-strand	108-109	2	51
β-strand	113-117	5	51
β-strand	123	1	52
β-strand	126-130	5	53
β-strand	141-151	11	53
β-strand	152	1	52
β-strand	157-160	4	54
α-helix	161-163	3
β-strand	169-171	3	53
α-helix	172-174	3
β-strand	175-177	3	53
β-strand	180-190	11	53
β-strand	200-205	6	54
β-strand	210-215	6	54

Chain F: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	55
β-strand	10-13	4	56
β-strand	19-25	7	55
β-strand	33-38	6	56
β-strand	44-49	6	56
β-strand	53-54	2	56
α-helix	55	1
β-strand	62-67	6	55
β-strand	70-75	6	55
β-strand	85-90	6	56
α-helix	96	1
β-strand	97-98	2	56
β-strand	102-106	5	56
β-strand	111	1	57
β-strand	114-118	5	58
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	58
β-strand	140	1	57
β-strand	145-150	6	59
β-strand	153-155	3	59
β-strand	159-163	5	58
β-strand	173-182	10	58
α-helix	183-186	4
β-strand	191-198	8	59
β-strand	201-210	10	59

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	60
α-helix	7-9	3
β-strand	10-12	3	61
β-strand	18-25	8	60
α-helix	29-31	3
β-strand	34-40	7	61
β-strand	44-51	8	61
β-strand	58-60	3	61
α-helix	62-64	3
β-strand	65	1	60
β-strand	68-73	6	60
α-helix	74-76	3
β-strand	78-83	6	60
α-helix	88-90	3
β-strand	92-98	7	61
β-strand	102	1	10
β-strand	108-109	2	61
β-strand	113-117	5	61
β-strand	123	1	62
β-strand	126-130	5	63
β-strand	141-151	11	63
β-strand	152	1	62
β-strand	157-160	4	64
β-strand	165	1	64
β-strand	169-171	3	63
α-helix	172-174	3
β-strand	175-177	3	63
β-strand	180-190	11	63
β-strand	200-205	6	64
β-strand	210-215	6	64

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	65
β-strand	10-13	4	66
β-strand	19-25	7	65
β-strand	33-38	6	66
β-strand	44-49	6	66
β-strand	53-54	2	66
α-helix	55	1
β-strand	62-67	6	65
β-strand	70-75	6	65
β-strand	85-90	6	66
α-helix	96	1
β-strand	97-98	2	66
β-strand	99	1	65
β-strand	102-106	5	66
β-strand	111	1	67
β-strand	114-118	5	68
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	68
β-strand	140	1	67
β-strand	145-150	6	69
β-strand	153-155	3	69
β-strand	159-163	5	68
α-helix	164-167	4
β-strand	173-182	10	68
α-helix	183-186	4
β-strand	191-198	8	69
β-strand	201-210	10	69

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-iib	A, C	protein	457	HOMO SAPIENS	P08514 (AlphaFold model)
Integrin beta-3	B, D	protein	472	HOMO SAPIENS	P05106 (AlphaFold model)
10E5 FAB heavy chain	E, H	protein	221	MUS MUSCULUS
10E5 FAB light chain	F, L	protein	214	MUS MUSCULUS
Rgd peptide	I, J	protein	6	HOMO SAPIENS

Sequence of entity 1 (A, C), FASTA

>3ZDY_1 INTEGRIN ALPHA-IIB (chains A, C)
LNLDPVQLTFYAGPNGSQFGFSLDFHKDSHGRVAIVVGAPRTLGPSQEETGGVFLCPWRA
EGGQCPSLLFDLRDETRNVGSQTLQTFKARQGLGASVVSWSDVIVACAPWQHWNVLEKTE
EAEKTPVGSCFLAQPESGRRAEYSPCRGNTLSRIYVENDFSWDKRYCEAGFSSVVTQAGE
LVLGAPGGYYFLGLLAQAPVADIFSSYRPGILLWHVSSQSLSFDSSNPEYFDGYWGYSVA
VGEFDGDLNTTEYVVGAPTWSWTLGAVEILDSYYQRLHRLRGEQMASYFGHSVAVTDVNG
DGRHDLLVGAPLYMESRADRKLAEVGRVYLFLQPRGPHALGAPSLLLTGTQLYGRFGSAI
APLGDLDRDGYNDIAVAAPYGGPSGRGQVLVFLGQSEGLRSRPSQVLDSPFPTGSAFGFS
LRGAVDIDDNGYPDLIVGAYGANQVAVYRAQPVVKAS

Sequence of entity 2 (B, D), FASTA

>3ZDY_2 INTEGRIN BETA-3 (chains B, D)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCE

Sequence of entity 3 (E, H), FASTA

>3ZDY_3 10E5 FAB HEAVY CHAIN (chains E, H)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYVHWVKQRPEQGLEWIGRIDPANGYTKY
DPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCVRPLYDYYAMDYWGQGTSVTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Sequence of entity 4 (F, L), FASTA

>3ZDY_4 10E5 FAB LIGHT CHAIN (chains F, L)
DILMTQSPSSMSVSLGDTVSITCHASQGISSNIGWLQQKPGKSFMGLIYYGTNLVDGVPS
RFSGSGSGADYSLTISSLDSEDFADYYCVQYAQLPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (I, J), FASTA

>3ZDY_5 RGD PEPTIDE (chains I, J)
GRGDSP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Complete Integrin Headpiece Opening in Eight Steps. Zhu, J., Zhu, J., Springer, T.A. J Cell Biol (2013) 201:1053. DOI 10.1083/JCB.201212037 · PubMed

Other PDB entries of the same protein (UniProt P08514 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SC4 1.85 Å, filamin complex-1
7UDH 2.0 Å, Integrin alpha IIB beta3 complex with BMS4-3
7UBR 2.05 Å, Integrin alpha IIB beta3 complex with GR144053
3T3P 2.2 Å, A Novel High Affinity Integrin alphaIIbbeta3 Receptor Antagonist That Unexpectedly…
7TMZ 2.2 Å, Integrin alpha IIB beta3 complex with BMS compound 4
3NIG 2.25 Å, The Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific…
7U9V 2.25 Å, Integrin alpha IIB beta3 complex with BMS4-1
3NID 2.3 Å, The Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3…
7L8P 2.35 Å, Integrin alphaIIbbeta3 in complex with sibrafiban
7UCY 2.35 Å, Integrin alpha IIB beta3 complex with gantofiban
3ZE2 2.35 Å, Integrin alphaIIB beta3 headpiece and RGD peptide complex
7UKT 2.37 Å, Integrin alpha IIB beta3 complex with BMS4.2

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