Research workbench
The crystal structure of the narghi mutant nari-K86A
Analyse The crystal structure of the narghi mutant nari-K86A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y5I
- Type
- protein
- Length
- 1,970 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Respiratory nitrate reductase 1 alpha chain; Respiratory nitrate reductase 1 beta chain…
- EC
- 1.7.99.4
- UniProt
- P09152, P11349, P11350
- Ligands
- SF4, MD1, HEM, F3S, 3PH, AGA, 6MO
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Respiratory nitrate reductase 1 alpha chain (EC 1.7.99.4) | protein | 1244 | 32% helix, 19% strand | P09152 |
| B | Respiratory nitrate reductase 1 beta chain (EC 1.7.99.4) | protein | 509 | 33% helix, 14% strand | P11349 |
| C | Respiratory nitrate reductase 1 gamma chain (EC 1.7.99.4) | protein | 217 | 79% helix, 2% strand | P11350 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- MD1 · Phosphoric acid 4-(2-amino-4-oxo-3,4,5,6,-tetrahydro-pteridin-6-yl)-2-hydroxy-3,4-dimercapto-but-3-en-yl ester guanylate ester · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C
- F3S · FE3-S4 cluster · ligand · chains B
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains B
- AGA · (1S)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(pentanoyloxy)methyl]ethyl octanoate · ligand · chains A, B, C
- 6MO · Molybdenum(vi) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.88 | 0.97 | 90 | MD1, 6MO, SF4 |
| 2 | 1182 | 0.86 | 0.86 | 82 | HEM |
| 3 | 386 | 0.79 | 0.88 | 42 | AGA |
| 4 | 100 | 0.78 | 0.98 | 29 | empty |
| 5 | 604 | 0.77 | 0.83 | 50 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6069 Ų buried · 117 hydrogen bonds · protein-protein
- B–C · 2640 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (formylation).
Compared structures
- 1Y5I · The crystal structure of the NarGHI mutant NarI-K86A · the same entry in another collection · chain A against A, TM-score 1.00
- P09152 · AlphaFold monomer V2.0 prediction for respiratory nitrate reductase 1 alpha chain (P09152) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P11349 · AlphaFold monomer V2.0 prediction for respiratory nitrate reductase 1 beta chain (P11349) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P11350 · AlphaFold monomer V2.0 prediction for respiratory nitrate reductase 1 gamma chain (P11350) · a predicted model of the same protein · chain C 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 P09152
- Every structure of UniProt P11349
- Every structure of UniProt P11350
- Elsewhere: RCSB PDB 1Y5I · PDBe 1Y5I · UniProt P09152 · UniProt P11349 · UniProt P11350
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