4G1M
Re-refinement of alpha V beta 3 structure
- PDB DOI: https://doi.org/10.2210/pdb4G1M/pdb
- Classification: PROTEIN BINDING
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No
- Deposited: 2012-07-10 Released: 2012-12-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.233
- R-Value Work: 0.179
- R-Value Observed: 0.182
This is version 2.0 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-V | 959 | Homo sapiens | Mutation(s): 0 Gene Names: ITGAV, MSK8, VNRA |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06756 (Homo sapiens) Explore P06756 Go to UniProtKB: P06756 | |||||
PHAROS: P06756 GTEx: ENSG00000138448 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06756 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Integrin beta-3 | 692 | 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 | |||||
| |||||
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| 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 | C | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, F, G, H, I D, F, G, H, I, J, K, L, M | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | E | 7 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | T [auth A], U [auth A], Y [auth B], Z [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| CA Query on CA | O [auth A] P [auth A] Q [auth A] R [auth A] S [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| NA Query on NA | V [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.233
- R-Value Work: 0.179
- R-Value Observed: 0.182
- Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 129.87 | α = 90 |
| b = 129.87 | β = 90 |
| c = 305.9 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| CNS | refinement |
| HKL-2000 | data collection |
| DENZO | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2012-12-12 Deposition Author(s): Springer, T.A., Mi, L., Zhu, J.
Revision History (Full details and data files)
- Version 1.0: 2012-12-12
Type: Initial release - Version 1.1: 2012-12-19
Changes: Database references - Version 1.2: 2019-08-14
Changes: Data collection, Derived calculations, Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
