Research workbench
Disulfide deficient mutant of vascular endothelial growth factor a (C57A and C102A)
Analyse Disulfide deficient mutant of vascular endothelial growth factor a (C57A and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MKG
- Type
- protein
- Length
- 376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Vascular endothelial growth factor a | protein | 94 | 12% helix, 57% strand | P15692 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.53 | 0.78 | 41 | empty |
| 2 | 100 | 0.40 | 0.76 | 22 | empty |
| 3 | 114 | 0.36 | 0.73 | 21 | empty |
| 4 | 83 | 0.36 | 0.76 | 19 | empty |
| 5 | 57 | 0.28 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1375 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1361 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 430 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 292 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1MKG · DISULFIDE DEFICIENT MUTANT OF VASCULAR ENDOTHELIAL GROWTH FACTOR A (C57A and C102A) · 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 0.93
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 1MKG · PDBe 1MKG · UniProt P15692
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