Research workbench
Crystal structure of sema domain of the met receptor in complex with Fab
Analyse Crystal structure of sema domain of the met receptor in complex with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I04
- Type
- protein
- Length
- 1,723 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor receptor; Fab heavy chain; Fab light chain
- EC
- 2.7.10.1
- UniProt
- P08581
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 442 | 5% helix, 47% strand | P08581 |
| H | Fab heavy chain | protein | 211 | 8% helix, 53% strand | — |
| L, D | Fab light chain | protein | 212 | 7% helix, 52% strand | — |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 432 | 5% helix, 47% strand | P08581 |
| C | Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.81 | 0.84 | 79 | empty |
| 2 | 1175 | 0.80 | 0.81 | 87 | empty |
| 3 | 684 | 0.70 | 0.77 | 81 | empty |
| 4 | 455 | 0.67 | 0.79 | 71 | empty |
| 5 | 718 | 0.65 | 0.74 | 64 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1794 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1669 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 22 hydrogen bonds · protein-protein
- A–L · 713 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 593 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6I04 · Crystal structure of Sema domain of the Met receptor in complex with FAB · 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
- Every structure of UniProt P08581
- Elsewhere: RCSB PDB 6I04 · PDBe 6I04 · UniProt P08581
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