MolNFT v1 · #103388 · protein
Crystal structure of M. tuberculosis in complex with bto - covalent adduct
4PFA · Probable decaprenylphosphoryl-beta-D-ribose oxidase: “Crystal structure of M. tuberculosis in complex with bto - covalent adduct”. X-ray diffraction, 2 ligands (FAD, N77), 4 pockets (best druggability 0.80). MolNFT v1 #103388 on…
- PDB
- 4PFA
- Type
- protein
- Length
- 843 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, N77
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 427 | 30% helix, 25% strand | P9WJF1 |
| B | Probable decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.-.-.-) | protein | 416 | 30% helix, 25% strand | P9WJF1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- N77 · 7-(hydroxyamino)-N-(pyridin-3-ylmethyl)-5-(trifluoromethyl)-1,3-benzothiazole-2-carboxamide 3-oxide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.80 | 0.84 | 79 | FAD, N77 |
| 2 | 696 | 0.80 | 0.84 | 82 | FAD, N77 |
| 3 | 618 | 0.66 | 0.76 | 62 | empty |
| 4 | 150 | 0.44 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 498 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4PFA · Crystal structure of M. tuberculosis in complex with BTO - covalent adduct · the same entry in another collection · chain B against B, 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 0.98
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 4PFA · PDBe 4PFA · UniProt P9WJF1
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