MolNFT v1 · #71669 · protein
Crystal structure of the periplasmic nitrate reductase from cupriavidus necator
3ML1: “Crystal structure of the periplasmic nitrate reductase from cupriavidus necator”. X-ray diffraction, 4 ligands (MGD, HEC, SF4), 6 pockets (best druggability 0.88). MolNFT v1 #71669 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ML1
- Type
- protein
- Length
- 908 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic nitrate reductase; Diheme cytochrome C napb
- EC
- 1.7.99.4, 1.9.6.1
- UniProt
- P39185, P39186
- Ligands
- MGD, HEC, SF4, MOS
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic nitrate reductase (EC 1.7.99.4) | protein | 799 | 35% helix, 20% strand | P39185 |
| B | Diheme cytochrome C napb (EC 1.9.6.1) | protein | 109 | 19% helix, 10% strand | P39186 |
Ligands and binding sites
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 2 copies · chains A
- HEC · Heme C · ligand · 2 copies · chains B, A
- SF4 · Iron/sulfur cluster · ligand · chains A
- MOS · Dioxothiomolybdenum(vi) ion · ligand · chains A
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 | 353 | 0.88 | 0.97 | 70 | MOS, MGD |
| 2 | 768 | 0.80 | 0.83 | 86 | HEC |
| 3 | 302 | 0.57 | 0.77 | 41 | empty |
| 4 | 80 | 0.35 | 0.75 | 17 | empty |
| 5 | 82 | 0.34 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3190 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 3ML1 · Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator · the same entry in another collection · chain A against A, TM-score 1.00
- P39185 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase (P39185) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P39186 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase, electron transfer… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P39185
- Every structure of UniProt P39186
- Elsewhere: RCSB PDB 3ML1 · PDBe 3ML1 · UniProt P39185 · UniProt P39186
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