MolNFT v1 · #38131 · protein
Crystal structure of the orf virus NZ2 variant of VEGF-E
2GNN · Vascular endothelial growth factor homolog: “Crystal structure of the orf virus NZ2 variant of VEGF-E”. X-ray diffraction, 4 ligands (BEN, NAG, CL), 4 pockets (best druggability 0.51). MolNFT v1 #38131 on GenesisL1: 3D structure…
- PDB
- 2GNN
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor homolog
- UniProt
- P52584
- Ligands
- BEN, NAG, CL, SO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor homolog | protein | 92 | 12% helix, 57% strand | P52584 |
| B | Vascular endothelial growth factor homolog | protein | 95 | 13% helix, 58% strand | P52584 |
| C | Vascular endothelial growth factor homolog | protein | 90 | 13% helix, 57% strand | P52584 |
| D | Vascular endothelial growth factor homolog | protein | 93 | 12% helix, 55% strand | P52584 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 3 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- CL · Chloride ion · ion · 3 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.51 | 0.76 | 39 | BEN |
| 2 | 52 | 0.36 | 0.79 | 16 | empty |
| 3 | 62 | 0.32 | 0.75 | 17 | GOL |
| 4 | 56 | 0.29 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1209 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1173 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 546 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 176 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2GNN · Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E · the same entry in another collection · chain A against A, TM-score 1.00
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 P52584
- Elsewhere: RCSB PDB 2GNN · PDBe 2GNN · UniProt P52584
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