MolNFT v1 · #182353 · protein
Cryo-EM MAP of the C-met II/HGF I/HGF II (K4 and sph) sub-complex
7MO9 · Hepatocyte growth factor: “Cryo-EM MAP of the C-met II/HGF I/HGF II (K4 and sph) sub-complex”. Electron microscopy, 2 ligands (SGN, IDS), 17 pockets (best druggability 0.73). MolNFT v1 #182353 on GenesisL1: 3D structure, binding…
- PDB
- 7MO9
- Type
- protein
- Length
- 1,247 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
- 17 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 254 | 8% helix, 20% strand | P14210 |
| D | Hepatocyte growth factor | protein | 305 | 11% helix, 27% strand | P14210 |
| E | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 688 | 7% helix, 40% 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.97 | 21 | empty |
| 2 | 168 | 0.70 | 0.89 | 44 | empty |
| 3 | 125 | 0.70 | 0.91 | 23 | empty |
| 4 | 658 | 0.69 | 0.77 | 44 | empty |
| 5 | 597 | 0.68 | 0.78 | 56 | empty |
Interfaces
2 interfaces between chains.
- D–E · 897 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 611 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide (disulfide).
Compared structures
- 7MO9 · Cryo-EM map of the c-MET II/HGF I/HGF II (K4 and SPH) sub-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 7MO9 · PDBe 7MO9 · UniProt P14210 · UniProt P08581
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