MolNFT v1 · #7094 · protein
Crystal structure of homoserine kinase complexed with ADP
1FWK: “Crystal structure of homoserine kinase complexed with ADP”. X-ray diffraction, 2 ligands (ADP, MG), 9 pockets (best druggability 0.74). MolNFT v1 #7094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FWK
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoserine kinase
- EC
- 2.7.1.39
- UniProt
- Q58504
- Ligands
- ADP, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Homoserine kinase (EC 2.7.1.39) | protein | 296 | 38% helix, 27% strand | Q58504 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.74 | 0.82 | 56 | ADP |
| 2 | 524 | 0.74 | 0.82 | 56 | ADP |
| 3 | 394 | 0.74 | 0.84 | 66 | empty |
| 4 | 323 | 0.72 | 0.85 | 42 | MG, ADP |
| 5 | 599 | 0.71 | 0.79 | 62 | ADP |
Interfaces
5 interfaces between chains.
- C–D · 1489 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1485 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 241 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 178 Ų buried · 1 hydrogen bond · protein-protein
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 Q58504
- Elsewhere: RCSB PDB 1FWK · PDBe 1FWK · UniProt Q58504
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