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1.9 ångström crystal structure of orotate phosphoribosyltransferase (pyre) francisella tularensis.
Analyse 1.9 ångström crystal structure of orotate phosphoribosyltransferase (pyre)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJD
- Type
- protein
- Length
- 826 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- Q5NHL5
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 209 | 42% helix, 23% strand | Q5NHL5 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 206 | 45% helix, 24% strand | Q5NHL5 |
| C | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 202 | 45% helix, 24% strand | Q5NHL5 |
| D | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 209 | 41% helix, 23% strand | Q5NHL5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.73 | 0.82 | 65 | empty |
| 2 | 101 | 0.67 | 0.91 | 19 | empty |
| 3 | 269 | 0.67 | 0.83 | 38 | empty |
| 4 | 99 | 0.66 | 0.90 | 20 | empty |
| 5 | 126 | 0.66 | 0.88 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1407 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1404 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 844 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3MJD · 1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransferase (pyrE) Francisella… · the same entry in another collection · chain A 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 Q5NHL5
- Elsewhere: RCSB PDB 3MJD · PDBe 3MJD · UniProt Q5NHL5
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