Research workbench
Conformation of CD1 nitrite reductase nirs without bound heme D1
Analyse Conformation of CD1 nitrite reductase nirs without bound heme D1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TPO
- Type
- protein
- Length
- 523 residues
- Chains
- 1
- 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
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase (EC 1.7.2.1, 1.7.99.1) | protein | 523 | 15% helix, 39% strand | P24474 |
Ligands and binding sites
- HEC · Heme C · ligand · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- BU3 · (R,R)-2,3-butanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.80 | 0.81 | 104 | HEC |
| 2 | 60 | 0.30 | 0.75 | 19 | empty |
| 3 | 58 | 0.29 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 2 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 6TPO · PDBe 6TPO · UniProt P24474
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