MolNFT v1 · #151857 · protein
Crystal structure of sema domain of the met receptor in complex with Fab
6I04 · Hepatocyte growth factor receptor: “Crystal structure of sema domain of the met receptor in complex with Fab”. X-ray diffraction, 18 pockets (best druggability 0.81). MolNFT v1 #151857 on GenesisL1: 3D structure, binding sites and…
- 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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