Research workbench
Crystal structure of orotate phosphoribosyltransferase (oprtase) from burkholderia cenocepacia
Analyse Crystal structure of orotate phosphoribosyltransferase (oprtase) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OHC
- Type
- protein
- Length
- 1,332 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- B4E589
- Ligands
- NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 221 | 43% helix, 20% strand | B4E589 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 222 | 42% helix, 21% strand | B4E589 |
| C | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 218 | 43% helix, 21% strand | B4E589 |
| D, F | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 225 | 42% helix, 20% strand | B4E589 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains B, D, E, F
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, D, E, B, C, F
- ACT · Acetate ion · additive · 6 copies · chains A, E, F, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.76 | 0.81 | 75 | ACT |
| 2 | 636 | 0.74 | 0.81 | 55 | ACT |
| 3 | 463 | 0.68 | 0.79 | 41 | EDO |
| 4 | 416 | 0.65 | 0.79 | 36 | EDO |
| 5 | 328 | 0.62 | 0.79 | 40 | ACT |
Interfaces
12 interfaces between chains.
- B–E · 1193 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1183 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1156 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 582 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4OHC · Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia… · the same entry in another collection · chain C against C, 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 B4E589
- Elsewhere: RCSB PDB 4OHC · PDBe 4OHC · UniProt B4E589
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