Research workbench
Cryo-EM structure of 1:1 C-met I/HGF I complex after focused 3D refinement of holo-complex
Analyse Cryo-EM structure of 1:1 C-met I/HGF I complex after focused 3D refinement of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MO8
- Type
- protein
- Length
- 1,250 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor; Hepatocyte growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P14210, P08581
- Ligands
- SGN, IDS
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 637 | 9% helix, 22% strand | P14210 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 613 | 8% helix, 37% strand | P08581 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 3 copies · chains A
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.78 | 0.79 | 98 | empty |
| 2 | 242 | 0.72 | 0.87 | 53 | empty |
| 3 | 662 | 0.71 | 0.78 | 45 | empty |
| 4 | 59 | 0.69 | 0.95 | 21 | empty |
| 5 | 678 | 0.67 | 0.76 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 2091 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 7MO8 · Cryo-EM structure of 1:1 c-MET I/HGF I complex after focused 3D refinement of holo-complex · 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 P14210
- Every structure of UniProt P08581
- Elsewhere: RCSB PDB 7MO8 · PDBe 7MO8 · UniProt P14210 · UniProt P08581
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