Research workbench
Crystal structure of vascular endothelial growth factor (VEGF8-109) with HH4, an ALPHA/BETA-peptide with irregular secondary structure
Analyse Crystal structure of vascular endothelial growth factor (VEGF8-109) with HH4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3O
- Type
- protein
- Length
- 219 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a; HH4
- UniProt
- P15692
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor a | protein | 96 | 11% helix, 63% strand | P15692 |
| B | Vascular endothelial growth factor a | protein | 95 | 12% helix, 63% strand | P15692 |
| C | HH4 | protein | 15 | 27% helix, 0% strand | — |
| D | HH4 | protein | 13 | 31% helix, 0% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.45 | 0.75 | 43 | empty |
| 2 | 96 | 0.34 | 0.73 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1330 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 407 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 7 disulfide (nonstandard, disulfide).
Compared structures
- 6D3O · Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with HH4, an… · 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 P15692
- Elsewhere: RCSB PDB 6D3O · PDBe 6D3O · UniProt P15692
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