4Z7N

Integrin alphaIIbbeta3 in complex with AGDV peptide

PDB DOI: https://doi.org/10.2210/pdb4Z7N/pdb

Classification: Membrane protein/Immune system
Organism(s): Homo sapiens, Mus musculus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2015-04-07 Released: 2015-12-16
Deposition Author(s): Lin, F.-Y., Zhu, J., Springer, T.A.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.253
R-Value Work: 0.230
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 301.43 kDa
Atom Count: 21,759
Modelled Residue Count: 2,709
Deposited Residue Count: 2,722
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-IIb	A, C	455	Homo sapiens	Mutation(s): 0 Gene Names: ITGA2B, GP2B, ITGAB
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens) Explore P08514 Go to UniProtKB: P08514
PHAROS: P08514 GTEx: ENSG00000005961
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08514
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B, D	469	Homo sapiens	Mutation(s): 0 Gene Names: ITGB3, GP3A
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens) Explore P05106 Go to UniProtKB: P05106
PHAROS: P05106 GTEx: ENSG00000259207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05106
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10E5 heavy chain	E, G [auth H]	219	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10E5 light chain	F, H [auth L]	214	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrapeptide ALA-GLY-ASP-VAL	I [auth G], J	4	Homo sapiens	Mutation(s): 0
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Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth I]	5		N-Glycosylation	Interactions Focus chain K [auth I] Interactions & Density Focus chain K [auth I]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K], N	2		N-Glycosylation	Interactions Focus chain L [auth K] Focus chain N Interactions & Density Focus chain L [auth K] Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	4		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain AA [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain AA [auth B]	AA [auth B], MA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain MA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain MA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain NA [auth L] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain NA [auth L] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A]	BA [auth C] HA [auth C] IA [auth C] NA [auth L] S [auth A] BA [auth C], HA [auth C], IA [auth C], NA [auth L], S [auth A], T [auth A], U [auth A], V [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain NA [auth L] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain NA [auth L] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A]	W [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain LA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain KA [auth D]	JA [auth D] KA [auth D] LA [auth D] X [auth B] Y [auth B] JA [auth D], KA [auth D], LA [auth D], X [auth B], Y [auth B], Z [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] O [auth A] DA [auth C], EA [auth C], FA [auth C], GA [auth C], O [auth A], P [auth A], Q [auth A], R [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] MOL2 format, chain CA [auth C]	CA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Interactions & Density Focus chain CA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.253
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 256.883	α = 90
b = 144.373	β = 90
c = 104.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-12-16

Deposition Author(s):

Lin, F.-Y.

Zhu, J.

Springer, T.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL103526

Revision History (Full details and data files)

Version 1.0: 2015-12-16
Type: Initial release
Version 1.1: 2016-03-09
Changes: Database references
Version 1.2: 2017-09-13
Changes: Advisory, Author supporting evidence, Database references, Derived calculations
Version 1.3: 2019-12-04
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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4Z7N

Integrin alphaIIbbeta3 in complex with AGDV peptide

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Entity Groups

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Entity ID: 5

Sequence Annotations

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Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)