Research workbench
Structure of the salmonella typhimurium nfnb dihydropteridine reductase
Analyse Structure of the salmonella typhimurium nfnb dihydropteridine reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HZN
- Type
- protein
- Length
- 1,751 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygen-insensitive NAD(P)H nitroreductase
- EC
- 1.-.-.-
- UniProt
- P15888
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 219 | 56% helix, 15% strand | P15888 |
| C, G | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 218 | 54% helix, 15% strand | P15888 |
| H | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 220 | 55% helix, 15% strand | P15888 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains C, E, G, H
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
- SIN · Succinic acid · additive · 44 copies · chains A, B, D, H, C, F, E, G
- MLI · Malonate ion · additive · 19 copies · chains A, B, C, D, H, E, F, G
- TLA · L(+)-tartaric acid · additive · 7 copies · chains A, B, G, C, D, E, F, H
- ACT · Acetate ion · additive · 3 copies · chains C, D, H, G
- FLC · Citrate anion · additive · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.87 | 0.88 | 141 | SIN, TLA, MLI |
| 2 | 454 | 0.82 | 0.89 | 56 | TLA, SIN |
| 3 | 248 | 0.80 | 0.93 | 42 | FLC, TLA, CL |
| 4 | 906 | 0.74 | 0.78 | 74 | SIN, MLI |
| 5 | 417 | 0.73 | 0.83 | 41 | MLI |
Interfaces
17 interfaces between chains.
- E–F · 3917 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 3865 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3861 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3826 Ų buried · 56 hydrogen bonds · protein-protein
- A–H · 543 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3HZN · Structure of the Salmonella typhimurium nfnB dihydropteridine reductase · the same entry in another collection · chain H against H, TM-score 1.00
- P15888 · AlphaFold monomer V2.0 prediction for oxygen-insensitive NAD(P)H nitroreductase (P15888) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P15888
- Elsewhere: RCSB PDB 3HZN · PDBe 3HZN · UniProt P15888
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