MolNFT v1 · #23411 · protein
Crystal structure of the Fab YADS1 complexed with H-VEGF
1TZH · Vascular endothelial growth factor a: “Crystal structure of the Fab YADS1 complexed with H-VEGF”. X-ray diffraction, 11 pockets (best druggability 0.59). MolNFT v1 #23411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1TZH
- Type
- protein
- Length
- 1,047 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a; Fab YADS1 light chain; Fab YADS1 heavy chain
- UniProt
- P15692
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V, W | Vascular endothelial growth factor a | protein | 94 | 13% helix, 64% strand | P15692 |
| A, L | Fab YADS1 light chain | protein | 210 | 6% helix, 51% strand | — |
| B | Fab YADS1 heavy chain | protein | 222 | 8% helix, 49% strand | — |
| H | Fab YADS1 heavy chain | protein | 217 | 7% helix, 50% strand | — |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.59 | 0.74 | 53 | empty |
| 2 | 391 | 0.57 | 0.74 | 49 | empty |
| 3 | 175 | 0.47 | 0.76 | 30 | empty |
| 4 | 110 | 0.43 | 0.77 | 18 | empty |
| 5 | 131 | 0.39 | 0.74 | 20 | empty |
Interfaces
11 interfaces between chains.
- L–H · 1786 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1734 Ų buried · 19 hydrogen bonds · protein-protein
- V–W · 1344 Ų buried · 13 hydrogen bonds · protein-protein
- V–H · 476 Ų buried · 5 hydrogen bonds · protein-protein
- W–B · 471 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1TZH · Crystal Structure of the Fab YADS1 Complexed with h-VEGF · the same entry in another collection · chain L against L, 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 V against A, TM-score 0.97
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 1TZH · PDBe 1TZH · UniProt P15692
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