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A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand
Analyse A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V3V
- Type
- protein
- Length
- 721 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.99
- Source
- DESULFOVIBRIO DESULFURICANS
- Molecule
- Periplasmic nitrate reductase
- EC
- 1.7.99.4
- UniProt
- P81186
- Ligands
- LCP, MGD, SF4, MO, UNX
- Pockets
- 3 · best druggability 0.89
Structure
x-ray diffraction · resolution 1.99 · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic nitrate reductase (EC 1.7.99.4) | protein | 721 | 35% helix, 20% strand | P81186 |
Ligands and binding sites
- LCP · Perchlorate ion · ligand · 4 copies · chains A
- 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
- SF4 · Iron/sulfur cluster · ligand · chains A
- MO · Molybdenum atom · metal · chains A
- UNX · Unknown atom or ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.89 | 0.96 | 81 | SF4, MO, MGD, UNX |
| 2 | 151 | 0.51 | 0.79 | 33 | LCP |
| 3 | 53 | 0.28 | 0.75 | 18 | empty |
Compared structures
- 2V3V · A new catalytic mechanism of periplasmic nitrate reductase from desulfovibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- P81186 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase (P81186) · a predicted model of the same protein · 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 P81186
- Elsewhere: RCSB PDB 2V3V · PDBe 2V3V · UniProt P81186
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