MolNFT v2 · #121299 · protein
Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21/n
5HHC · Vascular endothelial growth factor A: “Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group…”. X-ray diffraction at 2.1, 3 pockets (best druggability 0.46). MolNFT v2 #121299…
- PDB
- 5HHC
- Type
- protein
- Length
- 324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Molecule
- Vascular endothelial growth factor A; D- Vascular endothelial growth factor-A
- UniProt
- P15692
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 19% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vascular endothelial growth factor A | protein | 95 | 13% helix, 63% strand | P15692 |
| C | D- Vascular endothelial growth factor-A | protein | 66 | 20% helix, 45% strand | — |
| D | D- Vascular endothelial growth factor-A | protein | 68 | 26% helix, 44% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.46 | 0.74 | 45 | GOL |
| 2 | 61 | 0.26 | 0.72 | 14 | empty |
| 3 | 53 | 0.26 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1393 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 362 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 122 d-amino, 8 disulfide (D-amino acid, disulfide).
Compared structures
- 5HHC · Crystal structure of chemically synthesized heterochiral {RFX037 plus VEGF-a} protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P15692 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor a (P15692) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P15692
- Elsewhere: RCSB PDB 5HHC · PDBe 5HHC · UniProt P15692
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