MolNFT v1 · #181357 · protein
Structure of KD035, a VEGFR2 monoclonal antibody
7LSI · KD035 Fab heavy chain: “Structure of KD035, a VEGFR2 monoclonal antibody”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1 #181357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LSI
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KD035 Fab heavy chain; KD035 Fab light chain
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KD035 Fab heavy chain | protein | 209 | 9% helix, 52% strand | — |
| B | KD035 Fab heavy chain | protein | 214 | 9% helix, 50% strand | — |
| C | KD035 Fab light chain | protein | 210 | 8% helix, 50% strand | — |
| D | KD035 Fab light chain | protein | 209 | 8% helix, 49% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.72 | 0.76 | 84 | empty |
| 2 | 484 | 0.69 | 0.79 | 68 | empty |
| 3 | 339 | 0.65 | 0.80 | 38 | empty |
| 4 | 195 | 0.58 | 0.81 | 32 | empty |
| 5 | 199 | 0.55 | 0.79 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1699 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1559 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 999 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 317 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 118 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7LSI · Structure of KD035, a VEGFR2 monoclonal antibody · the same entry in another collection · chain A against A, 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 7LSI · PDBe 7LSI
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.