MolNFT v1 · #71344 · protein
Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from bacteroides thetaiotaomicron vpi-5482 at 2.10 a resolution (rhombohedral form)
3MBJ: “Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from bacteroides thetaiotaomicron…”. X-ray diffraction, 3 ligands (ZN, SO4, CL), 2 pockets (best druggability 0.77). MolNFT v1 #71344 on GenesisL1: 3D…
- PDB
- 3MBJ
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphomethylpyrimidine kinase
- UniProt
- Q89ZB9
- Ligands
- ZN, SO4, CL
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phosphomethylpyrimidine kinase | protein | 288 | 39% helix, 22% strand | Q89ZB9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.77 | 0.82 | 67 | ZN, SO4 |
| 2 | 50 | 0.26 | 0.74 | 11 | MRD |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3MBJ · Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q89ZB9
- Elsewhere: RCSB PDB 3MBJ · PDBe 3MBJ · UniProt Q89ZB9
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