Research workbench
The crystal structure of chemically synthesized VEGF-a
Analyse The crystal structure of chemically synthesized VEGF-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QTK
- Type
- protein
- Length
- 576 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor a | protein | 96 | 16% helix, 63% strand | P15692 |
| D, E | Vascular endothelial growth factor a | protein | 95 | 13% helix, 63% strand | P15692 |
| B, F | Vascular endothelial growth factor a | protein | 97 | 12% helix, 60% strand | P15692 |
| C | Vascular endothelial growth factor a | protein | 96 | 13% helix, 60% strand | P15692 |
Ligands and binding sites
- ACT · Acetate ion · additive · 8 copies · chains A, D, B, C, E, F
- TFA · trifluoroacetic acid · additive · 6 copies · chains A, D, B, E, F
- GOL · Glycerol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.69 | 0.78 | 64 | empty |
| 2 | 209 | 0.47 | 0.75 | 33 | empty |
| 3 | 94 | 0.36 | 0.75 | 19 | empty |
| 4 | 90 | 0.36 | 0.75 | 17 | empty |
| 5 | 104 | 0.35 | 0.74 | 22 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1423 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1393 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1371 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 363 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 335 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 3QTK · The crystal structure of chemically synthesized VEGF-A · 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 3QTK · PDBe 3QTK · UniProt P15692
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