Research workbench
Crystal structure of 1K1 mutant of hepatocyte growth FACTOR/SCATTER factor fragment NK1 in complex with heparin
Analyse Crystal structure of 1K1 mutant of hepatocyte growth FACTOR/SCATTER factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKP
- Type
- protein
- Length
- 688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor
- UniProt
- P14210
- Ligands
- SGN, IDS, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hepatocyte growth factor | protein | 173 | 10% helix, 28% strand | P14210 |
| D | Hepatocyte growth factor | protein | 169 | 9% helix, 32% strand | P14210 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 4 copies · chains C, A
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 3 copies · chains C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.75 | 0.82 | 66 | empty |
| 2 | 535 | 0.70 | 0.79 | 53 | empty |
| 3 | 184 | 0.54 | 0.79 | 37 | empty |
| 4 | 155 | 0.53 | 0.80 | 32 | empty |
| 5 | 105 | 0.52 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1241 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1116 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3MKP · Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1… · the same entry in another collection · chain C against C, 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 3MKP · PDBe 3MKP · UniProt P14210
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.