MolNFT v1 · #106112 · protein
Crystal structure of homoserine kinase from yersinia pestis NEPAL516, nysgrc target 032715
4RPF: “Crystal structure of homoserine kinase from yersinia pestis NEPAL516, nysgrc target 032715”. X-ray diffraction, 9 pockets (best druggability 0.66). MolNFT v1 #106112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RPF
- Type
- protein
- Length
- 929 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine kinase
- EC
- 2.7.1.39
- UniProt
- Q1CMW6
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Homoserine kinase (EC 2.7.1.39) | protein | 310 | 39% helix, 25% strand | Q1CMW6 |
| C | Homoserine kinase (EC 2.7.1.39) | protein | 309 | 39% helix, 22% strand | Q1CMW6 |
Ligands and binding sites
- CIT · Citric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.66 | 0.85 | 43 | CIT |
| 2 | 220 | 0.65 | 0.84 | 45 | CIT |
| 3 | 221 | 0.65 | 0.84 | 47 | CIT |
| 4 | 190 | 0.47 | 0.76 | 20 | empty |
| 5 | 83 | 0.43 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1600 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 799 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4RPF · Crystal structure of homoserine kinase from Yersinia pestis Nepal516, NYSGRC target 032715 · the same entry in another collection · chain A against A, TM-score 1.00
- Q1CMW6 · AlphaFold monomer V2.0 prediction for homoserine kinase (Q1CMW6) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q1CMW6
- Elsewhere: RCSB PDB 4RPF · PDBe 4RPF · UniProt Q1CMW6
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