Research workbench
Structure of B1, a monoclonal VEGFR2 antibody parental of KD035
Analyse Structure of B1, a monoclonal VEGFR2 antibody parental of KD035 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LSB
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B1 Fab heavy chain; B1 Fab light chain
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | B1 Fab heavy chain | protein | 215 | 7% helix, 50% strand | — |
| D | B1 Fab light chain | protein | 209 | 8% helix, 50% strand | — |
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 | 348 | 0.52 | 0.73 | 48 | empty |
| 2 | 107 | 0.40 | 0.76 | 23 | empty |
| 3 | 68 | 0.38 | 0.79 | 18 | empty |
| 4 | 71 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- B–D · 1720 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LSB · Structure of B1, a monoclonal VEGFR2 antibody parental of KD035 · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7LSB · PDBe 7LSB
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