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Cryo-EM structure of the C-met II/HGF I complex bound with hgf II in a rigid conformation
Analyse Cryo-EM structure of the C-met II/HGF I complex bound with hgf II in a rigid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MOA
- Type
- protein
- Length
- 1,580 residues
- Chains
- 3
- 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 0.74
Structure
electron microscopy · 3 distinct chains · 9% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 254 | 10% helix, 20% strand | P14210 |
| E | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 688 | 7% helix, 39% strand | P08581 |
| D | Hepatocyte growth factor | protein | 638 | 11% helix, 23% strand | P14210 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 6 copies · chains A, D
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 6 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.74 | 0.99 | 21 | empty |
| 2 | 216 | 0.71 | 0.87 | 48 | empty |
| 3 | 134 | 0.69 | 0.90 | 22 | empty |
| 4 | 660 | 0.69 | 0.77 | 54 | empty |
| 5 | 660 | 0.68 | 0.76 | 52 | empty |
Interfaces
3 interfaces between chains.
- E–D · 1193 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 645 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 320 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 7MOA · Cryo-EM structure of the c-MET II/HGF I complex bound with HGF II in a rigid conformation · 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 7MOA · PDBe 7MOA · UniProt P14210 · UniProt P08581
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