Research workbench
Crystal structure of anti-met Fab arm of amivantamab in complex with human met
Analyse Crystal structure of anti-met Fab arm of amivantamab in complex with human met in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVZ
- Type
- protein
- Length
- 946 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of anti-met Fab of amivantamab; Light chain of anti-met Fab of amivantamab…
- EC
- 2.7.10.1
- UniProt
- P08581
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of anti-met Fab of amivantamab | protein | 215 | 8% helix, 52% strand | — |
| L | Light chain of anti-met Fab of amivantamab | protein | 213 | 5% helix, 48% strand | — |
| M | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 518 | 8% helix, 41% strand | P08581 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains M
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains M
- FMT · Formic acid · additive · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.69 | 0.76 | 56 | empty |
| 2 | 559 | 0.66 | 0.77 | 59 | empty |
| 3 | 139 | 0.56 | 0.82 | 24 | empty |
| 4 | 340 | 0.54 | 0.74 | 49 | empty |
| 5 | 139 | 0.40 | 0.74 | 30 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1703 Ų buried · 7 hydrogen bonds · protein-protein
- L–M · 696 Ų buried · 11 hydrogen bonds · protein-protein
- H–M · 503 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6WVZ · Crystal structure of anti-MET Fab arm of amivantamab in complex with human MET · the same entry in another collection · chain H against H, 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 P08581
- Elsewhere: RCSB PDB 6WVZ · PDBe 6WVZ · UniProt P08581
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