MolNFT v1 · #115593 · protein
The structure of the NK1 fragment of HGF/SF complexed with hepes
5COE · Hepatocyte growth factor: “The structure of the NK1 fragment of HGF/SF complexed with hepes”. X-ray diffraction, 3 pockets (best druggability 0.71). MolNFT v1 #115593 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5COE
- Type
- protein
- Length
- 346 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor
- UniProt
- P14210
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 173 | 9% helix, 32% strand | P14210 |
| B | Hepatocyte growth factor | protein | 173 | 11% helix, 30% strand | P14210 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.71 | 0.80 | 58 | empty |
| 2 | 381 | 0.59 | 0.76 | 55 | empty |
| 3 | 96 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1253 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5COE · The structure of the NK1 fragment of HGF/SF complexed with HEPES · the same entry in another collection · chain A against A, TM-score 1.00
- P14210 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (P14210) · a predicted model of the same protein · chain A against A, TM-score 0.60
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
- Elsewhere: RCSB PDB 5COE · PDBe 5COE · UniProt P14210
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