Research workbench
Crystal structure of the NK2 fragment (31-290) of the mouse hepatocyte growth FACTOR/SCATTER factor
Analyse Crystal structure of the NK2 fragment (31-290) of the mouse hepatocyte growth… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IUA
- Type
- protein
- Length
- 2,016 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor
- UniProt
- Q08048
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hepatocyte growth factor | protein | 254 | 9% helix, 21% strand | Q08048 |
| G | Hepatocyte growth factor | protein | 246 | 5% helix, 21% strand | Q08048 |
| H | Hepatocyte growth factor | protein | 246 | 9% helix, 22% strand | Q08048 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, F, G, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 10 copies · chains A, E, B, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.82 | 0.83 | 108 | empty |
| 2 | 1067 | 0.82 | 0.83 | 95 | empty |
| 3 | 790 | 0.81 | 0.84 | 91 | empty |
| 4 | 591 | 0.77 | 0.84 | 59 | empty |
| 5 | 276 | 0.66 | 0.83 | 38 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1372 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1370 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 1342 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 1242 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 418 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide (disulfide).
Compared structures
- 4IUA · Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth… · the same entry in another collection · chain H against H, TM-score 1.00
- Q08048 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (Q08048) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 Q08048
- Elsewhere: RCSB PDB 4IUA · PDBe 4IUA · UniProt Q08048
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.