Research workbench
Structure of ddn, the deazaflavin-dependent nitroreductase from mycobacterium tuberculosis involved in bioreductive activation of pa- 824, with co-factor F420
Analyse Structure of ddn, the deazaflavin-dependent nitroreductase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5R
- Type
- protein
- Length
- 545 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deazaflavin-dependent nitroreductase
- EC
- 1.-.-.-
- UniProt
- P71854
- Ligands
- F42
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Deazaflavin-dependent nitroreductase (EC 1.-.-.-) | protein | 109 | 29% helix, 37% strand | P71854 |
Ligands and binding sites
- F42 · Coenzyme F420 · ligand · 5 copies · chains A, C, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.69 | 0.78 | 61 | F42 |
| 2 | 334 | 0.61 | 0.78 | 37 | F42 |
| 3 | 71 | 0.31 | 0.74 | 15 | empty |
| 4 | 79 | 0.31 | 0.74 | 20 | empty |
| 5 | 57 | 0.29 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–E · 449 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 412 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3R5R · Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium… · 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 P71854
- Elsewhere: RCSB PDB 3R5R · PDBe 3R5R · UniProt P71854
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.