Research workbench
Structural basis for the function of two anti-VEGF receptor antibodies
Analyse Structural basis for the function of two anti-VEGF receptor antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S36
- Type
- protein
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1121B light chain; 1121B heavy chain; Vascular endothelial growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P35968
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 1121B light chain | protein | 214 | 6% helix, 48% strand | — |
| H | 1121B heavy chain | protein | 214 | 6% helix, 53% strand | — |
| X | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 112 | 6% helix, 46% strand | P35968 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.54 | 0.74 | 40 | empty |
| 2 | 59 | 0.53 | 0.88 | 21 | empty |
| 3 | 112 | 0.46 | 0.79 | 30 | empty |
| 4 | 111 | 0.40 | 0.76 | 20 | empty |
| 5 | 50 | 0.28 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1818 Ų buried · 17 hydrogen bonds · protein-protein
- H–X · 714 Ų buried · 25 hydrogen bonds · protein-protein
- L–X · 346 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3S36 · 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 3S36 · PDBe 3S36 · UniProt P35968
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