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 
- 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 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Integrin alpha-IIb | 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Integrin beta-3 | 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Monoclonal antibody 10E5 heavy chain | E, G [auth H] | 219 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
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  | |
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 6 | |||||
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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 | ||
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 8 | |||||
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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 | ||
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 | AA [auth B], MA [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | BA [auth C] HA [auth C] IA [auth C] NA [auth L] S [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | W [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
MN Query on MN | JA [auth D] KA [auth D] LA [auth D] X [auth B] Y [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N | |||
CA Query on CA | DA [auth C] EA [auth C] FA [auth C] GA [auth C] O [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | CA [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
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 Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
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