Research workbench
CD1 nitrite reductase nirs with bound dihydro-heme D1
Analyse CD1 nitrite reductase nirs with bound dihydro-heme D1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TSI
- Type
- protein
- Length
- 1,080 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.2.1, 1.7.99.1
- UniProt
- P24474
- Ligands
- HEC, DHE, PO4, CL
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrite reductase (EC 1.7.2.1, 1.7.99.1) | protein | 540 | 16% helix, 38% strand | P24474 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- DHE · Heme D · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.85 | 0.86 | 114 | HEC, DHE |
| 2 | 1047 | 0.85 | 0.86 | 124 | HEC, DHE, PO4 |
| 3 | 463 | 0.83 | 0.90 | 53 | CL |
| 4 | 996 | 0.78 | 0.80 | 69 | empty |
| 5 | 161 | 0.44 | 0.75 | 23 | CL |
Interfaces
1 interface between chains.
- A–B · 3449 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
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 P24474
- Elsewhere: RCSB PDB 6TSI · PDBe 6TSI · UniProt P24474
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