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
- 3R5W
- Type
- protein
- Length
- 1,090 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deazaflavin-dependent nitroreductase
- EC
- 1.-.-.-
- UniProt
- P71854
- Ligands
- F42
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, K, L, M, N, O | Deazaflavin-dependent nitroreductase (EC 1.-.-.-) | protein | 109 | 30% helix, 37% strand | P71854 |
Ligands and binding sites
- F42 · Coenzyme F420 · ligand · 10 copies · chains A, M, B, N, C, K, D, L, E, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.79 | 0.82 | 72 | F42 |
| 2 | 1149 | 0.79 | 0.80 | 83 | F42 |
| 3 | 1003 | 0.79 | 0.80 | 87 | F42 |
| 4 | 459 | 0.73 | 0.82 | 41 | F42 |
| 5 | 564 | 0.73 | 0.80 | 56 | F42 |
Interfaces
16 interfaces between chains.
- M–N · 476 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 470 Ų buried · 6 hydrogen bonds · protein-protein
- K–O · 463 Ų buried · 4 hydrogen bonds · protein-protein
- D–L · 449 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 443 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3R5W · 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 3R5W · PDBe 3R5W · UniProt P71854
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