Research workbench
Crystal structure of the E. COLI pyrimidine nucleoside hydrolase yeik in complex with inosine
Analyse Crystal structure of the E. COLI pyrimidine nucleoside hydrolase yeik in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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