Research workbench
Cryo-EM structure of 2:2 C-MET/HGF holo-complex
Analyse Cryo-EM structure of 2:2 C-MET/HGF holo-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MO7
- Type
- protein
- Length
- 2,329 residues
- Chains
- 4
- 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 · 4 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Hepatocyte growth factor | protein | 305 | 12% helix, 29% strand | P14210 |
| E | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 688 | 7% helix, 41% strand | P08581 |
| A | Hepatocyte growth factor | protein | 637 | 9% helix, 23% strand | P14210 |
| B | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 699 | 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
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.78 | 0.80 | 106 | empty |
| 2 | 88 | 0.76 | 0.97 | 34 | empty |
| 3 | 1116 | 0.74 | 0.77 | 86 | empty |
| 4 | 185 | 0.73 | 0.90 | 42 | empty |
| 5 | 58 | 0.73 | 0.98 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2254 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 675 Ų buried · 11 hydrogen bonds · protein-protein
- E–A · 543 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide (disulfide).
Compared structures
- 7MO7 · Cryo-EM structure of 2:2 c-MET/HGF holo-complex · the same entry in another collection · chain D against D, 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 7MO7 · PDBe 7MO7 · UniProt P14210 · UniProt P08581
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