MolNFT v1 · #78242 · protein
Structural basis for the function of two anti-VEGF receptor antibodies
3S37 · 1121B Fab light chain: “Structural basis for the function of two anti-VEGF receptor antibodies”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #78242 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3S37
- Type
- protein
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1121B Fab light chain; 1121B Fab heavy chain; Vascular endothelial growth factor receptor…
- EC
- 2.7.10.1
- UniProt
- P35968
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 1121B Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| H | 1121B Fab heavy chain | protein | 209 | 6% helix, 52% strand | — |
| X | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 110 | 3% helix, 55% strand | P35968 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.65 | 0.75 | 73 | empty |
| 2 | 106 | 0.38 | 0.75 | 22 | empty |
| 3 | 102 | 0.37 | 0.75 | 26 | empty |
| 4 | 65 | 0.29 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1599 Ų buried · 9 hydrogen bonds · protein-protein
- H–X · 681 Ų buried · 16 hydrogen bonds · protein-protein
- L–X · 298 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3S37 · Structural basis for the function of two anti-VEGF receptor antibodies · the same entry in another collection · chain L against L, 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 P35968
- Elsewhere: RCSB PDB 3S37 · PDBe 3S37 · UniProt P35968
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