Research workbench
2.65 ångström resolution crystal structure of an orotate phosphoribosyltransferase from bacillus anthracis str. 'ames ancestor' in complex with 5-phospho-alpha-D-ribosyl diphosphate (prpp)
Analyse 2.65 ångström resolution crystal structure of an orotate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RV4
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- Q81WF6
- Ligands
- PRP
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 203 | 46% helix, 23% strand | Q81WF6 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 211 | 47% helix, 20% strand | Q81WF6 |
| C | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 202 | 47% helix, 21% strand | Q81WF6 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 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 | 46 | empty |
| 2 | 197 | 0.46 | 0.75 | 31 | PRP |
| 3 | 121 | 0.45 | 0.78 | 25 | empty |
| 4 | 177 | 0.45 | 0.75 | 25 | PRP |
| 5 | 137 | 0.42 | 0.75 | 22 | PRP |
Interfaces
2 interfaces between chains.
- A–B · 1255 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 229 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RV4 · 2.65 Angstrom Resolution Crystal Structure of an orotate phosphoribosyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81WF6 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase (Q81WF6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q81WF6
- Elsewhere: RCSB PDB 4RV4 · PDBe 4RV4 · UniProt Q81WF6
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