MolNFT v1 · #103391 · protein
Crystal structure of M. tuberculosis in complex with a cbt - non- covalent adduct
4PFD · Probable decaprenylphosphoryl-beta-D-ribose oxidase: “Crystal structure of M. tuberculosis in complex with a cbt - non- covalent adduct”. X-ray diffraction, 2 ligands (FAD, 2R2), 6 pockets (best druggability 0.82). MolNFT v1 #103391…
- PDB
- 4PFD
- Type
- protein
- Length
- 837 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable decaprenylphosphoryl-beta-D-ribose oxidase
- EC
- 1.-.-.-
- UniProt
- P9WJF1
- Ligands
- FAD, 2R2
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 427 | 31% helix, 26% strand | P9WJF1 |
| B | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 410 | 30% helix, 26% strand | P9WJF1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 2R2 · [4-(2-methoxyethyl)piperazin-1-yl][6-methyl-7-nitro-5-(trifluoromethyl)-1,3-benzothiazol-2-yl]methanone · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
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 | 790 | 0.82 | 0.85 | 89 | FAD, 2R2 |
| 2 | 613 | 0.80 | 0.85 | 59 | FAD, 2R2, IMD |
| 3 | 759 | 0.66 | 0.74 | 69 | empty |
| 4 | 195 | 0.46 | 0.74 | 23 | empty |
| 5 | 52 | 0.29 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 304 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4PFD · Crystal structure of M. tuberculosis in complex with a cBT - non-covalent adduct · the same entry in another collection · chain A against A, TM-score 1.00
- P9WJF1 · AlphaFold monomer V2.0 prediction for decaprenylphosphoryl-beta-D- ribose oxidase (P9WJF1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WJF1
- Elsewhere: RCSB PDB 4PFD · PDBe 4PFD · UniProt P9WJF1
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