MolNFT v1 · #19060 · protein
Crystal structure of the E.COLI pyrimidine nucleoside hydrolase yeik
1Q8F: “Crystal structure of the E.COLI pyrimidine nucleoside hydrolase yeik”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.74). MolNFT v1 #19060 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1Q8F
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine nucleoside hydrolase
- EC
- 3.2.2.8
- UniProt
- P33022
- Ligands
- CA
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyrimidine nucleoside hydrolase (EC 3.2.2.8) | protein | 308 | 43% helix, 19% strand | P33022 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.74 | 0.98 | 25 | CA, GOL |
| 2 | 65 | 0.71 | 0.97 | 20 | GOL |
| 3 | 62 | 0.71 | 0.98 | 20 | CA, GOL |
| 4 | 62 | 0.71 | 0.97 | 20 | CA, GOL |
| 5 | 246 | 0.53 | 0.76 | 51 | GOL |
Interfaces
6 interfaces between chains.
- B–D · 942 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 938 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 884 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 852 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Q8F · Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK · the same entry in another collection · chain A against A, TM-score 1.00
- P33022 · AlphaFold monomer V2.0 prediction for pyrimidine-specific ribonucleoside hydrolase rihb… · a predicted model of the same protein · 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 P33022
- Elsewhere: RCSB PDB 1Q8F · PDBe 1Q8F · UniProt P33022
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