Research workbench
Structure of a deazaflavin-dependent nitroreductase from nocardia farcinica, with co-factor F420
Analyse Structure of a deazaflavin-dependent nitroreductase from nocardia farcinica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5Y
- Type
- protein
- Length
- 565 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q5YUF0
- Ligands
- F42
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative uncharacterized protein | protein | 141 | 32% helix, 33% strand | Q5YUF0 |
| D | Putative uncharacterized protein | protein | 142 | 32% helix, 33% strand | Q5YUF0 |
Ligands and binding sites
- F42 · Coenzyme F420 · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.59 | 0.78 | 35 | F42 |
| 2 | 320 | 0.59 | 0.77 | 37 | F42 |
| 3 | 314 | 0.58 | 0.77 | 34 | F42 |
| 4 | 267 | 0.58 | 0.78 | 35 | F42 |
| 5 | 193 | 0.49 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 503 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3R5Y · Structure of a Deazaflavin-dependent nitroreductase from Nocardia farcinica, with… · 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 Q5YUF0
- Elsewhere: RCSB PDB 3R5Y · PDBe 3R5Y · UniProt Q5YUF0
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