MolNFT v1 · #58649 · protein
Crystal structure of the E. COLI pyrimidine nucleoside hydrolase yeik in complex with inosine
3B9X · Pyrimidine-specific ribonucleoside hydrolase rihb: “Crystal structure of the E. COLI pyrimidine nucleoside hydrolase yeik in complex with inosine”. X-ray diffraction, 3 ligands (NOS, TAM, CA), 12 pockets (best druggability 0.73).…
- PDB
- 3B9X
- Type
- protein
- Length
- 1,202 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-specific ribonucleoside hydrolase rihb
- EC
- 3.2.2.8
- UniProt
- P33022
- Ligands
- NOS, TAM, CA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrimidine-specific ribonucleoside hydrolase rihb (EC 3.2.2.8) | protein | 309 | 41% helix, 18% strand | P33022 |
| B | Pyrimidine-specific ribonucleoside hydrolase rihb (EC 3.2.2.8) | protein | 303 | 41% helix, 18% strand | P33022 |
| C | Pyrimidine-specific ribonucleoside hydrolase rihb (EC 3.2.2.8) | protein | 283 | 39% helix, 19% strand | P33022 |
| D | Pyrimidine-specific ribonucleoside hydrolase rihb (EC 3.2.2.8) | protein | 307 | 41% helix, 19% strand | P33022 |
Ligands and binding sites
- NOS · Inosine · ligand · 4 copies · chains A, B, C, D
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.73 | 0.98 | 22 | CA, NOS |
| 2 | 245 | 0.70 | 0.86 | 31 | NOS |
| 3 | 68 | 0.69 | 0.96 | 19 | NOS |
| 4 | 231 | 0.53 | 0.77 | 32 | empty |
| 5 | 197 | 0.53 | 0.78 | 33 | CA, NOS |
Interfaces
6 interfaces between chains.
- B–D · 936 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 887 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 887 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 866 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3B9X · Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P33022 · AlphaFold monomer V2.0 prediction for pyrimidine-specific ribonucleoside hydrolase rihb… · a predicted model of the same protein · chain C 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 3B9X · PDBe 3B9X · UniProt P33022
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