Research workbench
Crystal structures of NK1-heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the met receptor
Analyse Crystal structures of NK1-heparin complexes reveal the basis for NK1 activity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GMO
- Type
- protein
- Length
- 1,369 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor
- UniProt
- P14210
- Ligands
- IDS, SGN, SO4
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hepatocyte growth factor | protein | 172 | 10% helix, 27% strand | P14210 |
| E, F | Hepatocyte growth factor | protein | 173 | 10% helix, 29% strand | P14210 |
| G | Hepatocyte growth factor | protein | 164 | 11% helix, 28% strand | P14210 |
| H | Hepatocyte growth factor | protein | 171 | 9% helix, 26% strand | P14210 |
Ligands and binding sites
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 21 copies · chains A, B, H, F, C, G
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 21 copies · chains A, B, H, F, C, G
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 8 copies · chains A, C, B, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.73 | 0.81 | 67 | empty |
| 2 | 529 | 0.72 | 0.81 | 69 | empty |
| 3 | 506 | 0.72 | 0.81 | 57 | empty |
| 4 | 779 | 0.71 | 0.77 | 80 | EPE |
| 5 | 510 | 0.68 | 0.79 | 56 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1185 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1140 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1038 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 302 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 1GMO · Crystal structures of NK1-heparin complexes reveal the basis for NK1 activity and enable… · the same entry in another collection · chain H against H, TM-score 1.00
- P14210 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (P14210) · a predicted model of the same protein · chain G against A, TM-score 0.61
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 1GMO · PDBe 1GMO · UniProt P14210
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