Download MendeleyStructural Basis for the Bivalent Glycosylated Human VEGF-A121 and VEGF-A165 in recruiment of Receptor and Co-receptor
Shen, S.T., Huang, P.T., Shuau, Y.S., Lee, Y.M., Chen, Y.J., Liaw, Y.C., Lou, K.L.To be published.
4KZN
crystal structure of human VEGF-A receptor binding domain
- PDB DOI: https://doi.org/10.2210/pdb4KZN/pdb
- Classification: HORMONE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No
- Deposited: 2013-05-30 Released: 2014-06-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.218
- R-Value Work: 0.179
- R-Value Observed: 0.183
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Vascular endothelial growth factor A | 104 | Homo sapiens | Mutation(s): 0 Gene Names: VEGFA, VEGF |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15692 (Homo sapiens) Explore P15692 Go to UniProtKB: P15692 | |||||
PHAROS: P15692 GTEx: ENSG00000112715 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P15692 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P15692-13 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | B | 6 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | C [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | D [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.218
- R-Value Work: 0.179
- R-Value Observed: 0.183
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.573 | α = 90 |
| b = 32.014 | β = 92.99 |
| c = 42.981 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| RESOLVE | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-06-04 Deposition Author(s): Liaw, Y.C.
Revision History (Full details and data files)
- Version 1.0: 2014-06-04
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
