MolNFT v1 · #121077 · protein
Crystal structure of mycobacterium tuberculosis H37RV orotate phosphoribosyltransferase in complex with FE(III) dicitrate
5HKI: “Crystal structure of mycobacterium tuberculosis H37RV orotate phosphoribosyltransferase in complex with…”. X-ray diffraction, 1 ligand (6ZJ), 6 pockets (best druggability 0.72). MolNFT v1 #121077 on GenesisL1: 3D structure, binding…
- PDB
- 5HKI
- Type
- protein
- Length
- 686 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- P9WHK9
- Ligands
- 6ZJ
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 175 | 36% helix, 29% strand | P9WHK9 |
| B, C | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 168 | 37% helix, 27% strand | P9WHK9 |
Ligands and binding sites
- 6ZJ · Iron(III) dicitrate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.72 | 0.77 | 58 | 6ZJ |
| 2 | 371 | 0.71 | 0.83 | 39 | empty |
| 3 | 492 | 0.62 | 0.75 | 58 | 6ZJ |
| 4 | 98 | 0.36 | 0.75 | 32 | empty |
| 5 | 94 | 0.35 | 0.75 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1304 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1296 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HKI · Crystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WHK9 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase (P9WHK9) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P9WHK9
- Elsewhere: RCSB PDB 5HKI · PDBe 5HKI · UniProt P9WHK9
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