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The structure of the NK1 fragment of HGF/SF complexed with mes
Analyse The structure of the NK1 fragment of HGF/SF complexed with mes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CS9
- 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
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 172 | 12% helix, 31% strand | P14210 |
| B | Hepatocyte growth factor | protein | 174 | 11% helix, 30% strand | P14210 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.69 | 0.80 | 61 | empty |
| 2 | 207 | 0.51 | 0.77 | 40 | empty |
| 3 | 99 | 0.51 | 0.82 | 32 | empty |
| 4 | 88 | 0.36 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1215 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
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 5CS9 · PDBe 5CS9 · UniProt P14210
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