Research workbench
2.1 ångström resolution crystal structure of an orotate phosphoribosyltransferase (pyre) from vibrio cholerae O1 biovar eltor str. N16961
Analyse 2.1 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
- 3N2L
- Type
- protein
- Length
- 1,488 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- Q9KVD5
- Ligands
- CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 205 | 45% helix, 25% strand | Q9KVD5 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 175 | 43% helix, 27% strand | Q9KVD5 |
| C | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 193 | 48% helix, 25% strand | Q9KVD5 |
| D | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 170 | 45% helix, 26% strand | Q9KVD5 |
| F | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 177 | 44% helix, 27% strand | Q9KVD5 |
| G | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 194 | 47% helix, 25% strand | Q9KVD5 |
| H | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 169 | 46% helix, 27% strand | Q9KVD5 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.81 | 0.82 | 77 | empty |
| 2 | 1109 | 0.80 | 0.82 | 77 | empty |
| 3 | 257 | 0.60 | 0.79 | 39 | empty |
| 4 | 397 | 0.56 | 0.74 | 60 | empty |
| 5 | 97 | 0.55 | 0.84 | 21 | empty |
Interfaces
11 interfaces between chains.
- E–G · 1873 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1804 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1408 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1407 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1389 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3N2L · 2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE)… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9KVD5 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase (Q9KVD5) · a predicted model of the same protein · chain H against A, TM-score 0.96
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 Q9KVD5
- Elsewhere: RCSB PDB 3N2L · PDBe 3N2L · UniProt Q9KVD5
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