MolNFT v1 · #96439 · protein
2.06 ångström resolution crystal structure of phosphomethylpyrimidine kinase (THID)FROM clostridium difficile 630
4JJP: “2.06 ångström resolution crystal structure of phosphomethylpyrimidine kinase (THID)FROM clostridium difficile…”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #96439 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JJP
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine kinase
- EC
- 2.7.4.7
- UniProt
- Q186F5
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 231 | 43% helix, 24% strand | Q186F5 |
| B | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 217 | 45% helix, 26% strand | Q186F5 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.58 | 0.76 | 51 | empty |
| 2 | 110 | 0.47 | 0.80 | 27 | empty |
| 3 | 108 | 0.36 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4JJP · 2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from… · 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 Q186F5
- Elsewhere: RCSB PDB 4JJP · PDBe 4JJP · UniProt Q186F5
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