MolNFT v1 · #64511 · protein
Crystal structure of the E.COLI riha pyrimidine nucleosidase bound to a iminoribitol-based inhibitor
3G5I · Pyrimidine-specific ribonucleoside hydrolase riha: “Crystal structure of the E.COLI riha pyrimidine nucleosidase bound to a iminoribitol-based inhibitor”. X-ray diffraction, 2 ligands (DNB, CA), 17 pockets (best druggability 0.66).…
- PDB
- 3G5I
- Type
- protein
- Length
- 1,197 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine-specific ribonucleoside hydrolase riha
- EC
- 3.2.2.8
- UniProt
- P41409
- Ligands
- DNB, CA
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrimidine-specific ribonucleoside hydrolase riha (EC 3.2.2.8) | protein | 305 | 38% helix, 19% strand | P41409 |
| B | Pyrimidine-specific ribonucleoside hydrolase riha (EC 3.2.2.8) | protein | 295 | 40% helix, 20% strand | P41409 |
| C | Pyrimidine-specific ribonucleoside hydrolase riha (EC 3.2.2.8) | protein | 293 | 39% helix, 20% strand | P41409 |
| D | Pyrimidine-specific ribonucleoside hydrolase riha (EC 3.2.2.8) | protein | 304 | 39% helix, 20% strand | P41409 |
Ligands and binding sites
- DNB · (2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.66 | 0.80 | 36 | CA, DNB |
| 2 | 264 | 0.63 | 0.81 | 29 | CA, DNB |
| 3 | 177 | 0.59 | 0.82 | 36 | empty |
| 4 | 244 | 0.58 | 0.79 | 30 | DNB |
| 5 | 220 | 0.49 | 0.75 | 25 | DNB |
Interfaces
6 interfaces between chains.
- B–D · 1291 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1280 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 894 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 886 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3G5I · Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a… · the same entry in another collection · chain D against D, TM-score 1.00
- P41409 · AlphaFold monomer V2.0 prediction for pyrimidine-specific ribonucleoside hydrolase riha… · a predicted model of the same protein · chain B 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 P41409
- Elsewhere: RCSB PDB 3G5I · PDBe 3G5I · UniProt P41409
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.