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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
- 2JIR
- Type
- protein
- Length
- 720 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic nitrate reductase
- EC
- 1.7.99.4
- UniProt
- P81186
- Ligands
- MGD, SF4, MO, CYN, NO2
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic nitrate reductase (EC 1.7.99.4) | protein | 720 | 35% helix, 19% strand | P81186 |
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
- SF4 · Iron/sulfur cluster · ligand · chains A
- MO · Molybdenum atom · metal · chains A
- CYN · Cyanide ion · ion · chains A
- NO2 · Nitrite ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.88 | 0.96 | 72 | MO, MGD |
| 2 | 112 | 0.45 | 0.78 | 25 | empty |
| 3 | 62 | 0.33 | 0.76 | 14 | empty |
| 4 | 71 | 0.33 | 0.75 | 14 | empty |
| 5 | 51 | 0.27 | 0.75 | 18 | empty |
Compared structures
- 2JIR · 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 2JIR · PDBe 2JIR · UniProt P81186
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