MolNFT v1 · #54638 · protein
Crystal structure of vascular endothelial growth factor D
2XV7: “Crystal structure of vascular endothelial growth factor D”. X-ray diffraction, 3 ligands (NAG, BMA, MAN). MolNFT v1 #54638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XV7
- Type
- protein
- Length
- 104 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor D
- UniProt
- O43915
- Ligands
- NAG, BMA, MAN
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor D | protein | 104 | 22% helix, 49% strand | O43915 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2XV7 · Crystal structure of vascular endothelial growth factor D · the same entry in another collection · chain A against A, TM-score 1.00
- O43915 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor D (O43915) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O43915
- Elsewhere: RCSB PDB 2XV7 · PDBe 2XV7 · UniProt O43915
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