2VDN
Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide
- PDB DOI: https://doi.org/10.2210/pdb2VDN/pdb
- Entry: 2VDN supersedes: 1TY6
- Classification: CELL ADHESION/IMMUNE SYSTEM
- Organism(s): Homo sapiens, synthetic construct, Mus musculus
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2007-10-10 Released: 2008-09-02 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.213 
- R-Value Work: 0.163 
- R-Value Observed: 0.166 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
INTEGRIN ALPHA-IIB | 452 | Homo sapiens | Mutation(s): 0  | ||
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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
INTEGRIN BETA-3 | 461 | Homo sapiens | Mutation(s): 0  | ||
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: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
EPTIFIBATIDE | 8 | synthetic construct | Mutation(s): 0  | ||
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 HEAVY CHAIN | D [auth H] | 221 | 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: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN | E [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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Oligosaccharides
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F [auth D] | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC |
Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G [auth E] | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G09609EN GlyCosmos:  G09609EN GlyGen:  G09609EN |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | M [auth A], N [auth A], S [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | H [auth A], O [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CA Query on CA | I [auth A] J [auth A] K [auth A] L [auth A] Q [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
MG Query on MG | P [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
HRG Query on HRG | C | L-PEPTIDE LINKING | C7 H16 N4 O2 | ARG |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.213 
- R-Value Work: 0.163 
- R-Value Observed: 0.166 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 149.593 | α = 90 |
b = 149.593 | β = 90 |
c = 175.683 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
Entry History 
Deposition Data
- Released Date: 2008-09-02  Deposition Author(s): Springer, T.A., Zhu, J., Xiao, T.
- This entry supersedes: 1TY6
Revision History (Full details and data files)
- Version 1.0: 2008-09-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2016-12-28
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary - Version 1.3: 2019-01-30
Changes: Data collection, Experimental preparation, Other - Version 1.4: 2019-02-06
Changes: Data collection, Experimental preparation - Version 1.5: 2019-11-20
Changes: Advisory, Derived calculations, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary