MolNFT v1 · #151149 · protein
M tuberculosis DPRE1 in complex with BTZ043
6HEZ · Decaprenylphosphoryl-beta-D-ribose oxidase: “M tuberculosis DPRE1 in complex with BTZ043”. X-ray diffraction, 2 ligands (0SK, FAD), 6 pockets (best druggability 0.81). MolNFT v1 #151149 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HEZ
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decaprenylphosphoryl-beta-D-ribose oxidase
- EC
- 1.1.98.3
- UniProt
- P9WJF1
- Ligands
- 0SK, FAD
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 427 | 31% helix, 26% strand | P9WJF1 |
| B | Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) | protein | 416 | 30% helix, 26% strand | P9WJF1 |
Ligands and binding sites
- 0SK · 8-(hydroxyamino)-2-[(2S)-2-methyl-1,4-dioxa-8-azaspiro[4.5]dec-8-yl]-6-(trifluoromethyl)-4H-1,3-benzothiazin-4-one · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 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 | 839 | 0.81 | 0.84 | 97 | 0SK, FAD |
| 2 | 611 | 0.80 | 0.85 | 78 | 0SK, FAD |
| 3 | 425 | 0.55 | 0.73 | 47 | empty |
| 4 | 58 | 0.47 | 0.84 | 23 | empty |
| 5 | 50 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 464 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 6HEZ · PDBe 6HEZ · UniProt P9WJF1
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