2VDR: Integrin AlphaIIbBeta3 Headpiece

Integrin AlphaIIbBeta3 Headpiece Bound to a chimeric Fibrinogen Gamma chain peptide, LGGAKQRGDV. Determined by X-ray diffraction at 2.4 Å resolution. Released 2 Sept 2008.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: HOMO SAPIENS, MUS MUSCULUS
Chains: 5
Atoms: 11,884
Mol. weight: 151.36 kDa
Ligands: CA, MG, NAG
Released: 2 Sept 2008

Explore 2VDR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VDR contains 47 α-helices and 117 β-strands across 5 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	67-68	2	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
α-helix	313	1
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
β-strand	450	1	1

Chain B: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
β-strand	23-26	4	16
β-strand	38-40	3	16
α-helix	41-46	6
β-strand	54-55	2	16
β-strand	60-65	6	17
α-helix	67-70	4
β-strand	83-84	2	18
β-strand	87-92	6	17
β-strand	97-105	9	18
α-helix	109-111	3
β-strand	112-119	8	19
α-helix	122-127	6
α-helix	128-145	18
β-strand	149-156	8	19
α-helix	171-174	4
α-helix	178-180	3
α-helix	185-187	3
β-strand	190-197	8	19
α-helix	200-208	9
β-strand	217	1	20
β-strand	220	1	21
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	19
β-strand	254	1	21
α-helix	259-263	5
α-helix	268-269	2
β-strand	280	1	19
α-helix	288-291	4
α-helix	292-301	10
β-strand	305-311	7	19
α-helix	312-314	3
α-helix	315-322	8
β-strand	329-333	5	19
α-helix	338-349	12
β-strand	353-356	4	22
β-strand	357-360	4	17
β-strand	366-373	8	18
β-strand	379-381	3	18
β-strand	385-389	5	22
β-strand	394-403	10	18
β-strand	411-418	8	17
β-strand	425-431	7	17
α-helix	436-440	5

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	409	1	20

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	23
α-helix	7-9	3
β-strand	10-12	3	24
β-strand	18-25	8	23
α-helix	29-31	3
β-strand	34-40	7	24
β-strand	44-52	9	24
β-strand	57-60	4	24
β-strand	65	1	23
β-strand	68-73	6	23
β-strand	78-83	6	23
α-helix	88-90	3
β-strand	92-98	7	24
β-strand	102	1	10
β-strand	108-109	2	24
β-strand	113-117	5	24
α-helix	120-122	3
β-strand	123	1	25
α-helix	124-125	2
β-strand	126-130	5	26
α-helix	131-133	3
β-strand	141-151	11	26
β-strand	152	1	25
β-strand	157-160	4	27
α-helix	161-163	3
β-strand	169-171	3	26
α-helix	172-174	3
β-strand	175-177	3	26
β-strand	180-190	11	26
β-strand	200-205	6	27
α-helix	206-208	3
β-strand	210-215	6	27

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-13	4	24
β-strand	19-25	7	28
β-strand	33-38	6	24
β-strand	44-49	6	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	28
β-strand	70-75	6	28
α-helix	80-82	3
β-strand	85-90	6	24
α-helix	96	1
β-strand	97-98	2	24
β-strand	102-106	5	24
β-strand	111	1	29
α-helix	112-113	2
β-strand	114-118	5	30
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	30
β-strand	140	1	29
β-strand	145-150	6	31
β-strand	153-154	2	31
β-strand	159-163	5	30
α-helix	164-167	4
β-strand	173-182	10	30
α-helix	183-186	4
β-strand	191-197	7	31
α-helix	204	1
β-strand	205-210	6	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-iib	A	protein	452	HOMO SAPIENS	P08514 (AlphaFold model)
Integrin beta-3	B	protein	461	HOMO SAPIENS	P05106 (AlphaFold model)
Fibrinogen	C	protein	10	HOMO SAPIENS	P02679 (AlphaFold model)
Monoclonal antibody 10E5 heavy chain	H	protein	221	MUS MUSCULUS
Monoclonal antibody 10E5 light chain	L	protein	214	MUS MUSCULUS	P01837 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2VDR_1 INTEGRIN ALPHA-IIB (chains A)
LNLDPVQLTFYAGPNGSQFGFSLDFHKDSHGRVAIVVGAPRTLGPSQEETGGVFLCPWRA
EGGQCPSLLFDLRDETRNVGSQTLQTFKARQGLGASVVSWSDVIVACAPWQHWNVLEKTE
EAEKTPVGSCFLAQPESGRRAEYSPCRGNTLSRIYVENDFSWDKRYCEAGFSSVVTQAGE
LVLGAPGGYYFLGLLAQAPVADIFSSYRPGILLWHVSSQSLSFDSSNPEYFDGYWGYSVA
VGEFDGDLNTTEYVVGAPTWSWTLGAVEILDSYYQRLHRLRGEQMASYFGHSVAVTDVNG
DGRHDLLVGAPLYMESRADRKLAEVGRVYLFLQPRGPHALGAPSLLLTGTQLYGRFGSAI
APLGDLDRDGYNDIAVAAPYGGPSGRGQVLVFLGQSEGLRSRPSQVLDSPFPTGSAFGFS
LRGAVDIDDNGYPDLIVGAYGANQVAVYRAQP

Sequence of entity 2 (B), FASTA

>2VDR_2 INTEGRIN BETA-3 (chains B)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCR

Sequence of entity 3 (C), FASTA

>2VDR_3 FIBRINOGEN (chains C)
LGGAKQRGDV

Sequence of entity 4 (H), FASTA

>2VDR_4 MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN (chains H)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYVHWVKQRPEQGLEWIGRIDPANGYTKY
DPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCVRPLYDYYAMDYWGQGTSVTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Sequence of entity 5 (L), FASTA

>2VDR_5 MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN (chains L)
DILMTQSPSSMSVSLGDTVSITCHASQGISSNIGWLQQKPGKSFMGLIYYGTNLVDGVPS
RFSGSGSGADYSLTISSLDSEDFADYYCVQYAQLPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3. Springer, T.A., Zhu, J., Xiao, T. J Cell Biol (2008) 182:791. DOI 10.1083/JCB.200801146 · 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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