Research workbench
Crystal structure of the Fab YADS2 complexed with H-VEGF
Analyse Crystal structure of the Fab YADS2 complexed with H-VEGF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TZI
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab YADS2 light chain; Fab YADS2 heavy chain; Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab YADS2 light chain | protein | 214 | 5% helix, 51% strand | — |
| B | Fab YADS2 heavy chain | protein | 222 | 7% helix, 52% strand | — |
| V | Vascular endothelial growth factor a | protein | 97 | 12% helix, 61% strand | P15692 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.56 | 0.76 | 38 | empty |
| 2 | 318 | 0.53 | 0.74 | 44 | empty |
| 3 | 85 | 0.39 | 0.77 | 17 | empty |
| 4 | 106 | 0.33 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2040 Ų buried · 13 hydrogen bonds · protein-protein
- B–V · 127 Ų buried · 0 hydrogen bonds · protein-protein
- A–V · 118 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1TZI · Crystal Structure of the Fab YADS2 Complexed with h-VEGF · the same entry in another collection · chain V against V, 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 0.95
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 1TZI · PDBe 1TZI · UniProt P15692
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