Research workbench
Cryoem MAP and model of nitrite reductase at pH 8.1
Analyse Cryoem MAP and model of nitrite reductase at pH 8.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KNG
- Type
- protein
- Length
- 1,002 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- P25006
- Ligands
- CU
- Pockets
- 17 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 334 | 10% helix, 42% strand | P25006 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.82 | 0.86 | 49 | empty |
| 2 | 329 | 0.81 | 0.91 | 32 | empty |
| 3 | 106 | 0.77 | 0.97 | 18 | empty |
| 4 | 109 | 0.77 | 0.96 | 19 | empty |
| 5 | 99 | 0.76 | 0.96 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2156 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2150 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2140 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6KNG · CryoEM map and model of Nitrite Reductase at pH 8.1 · the same entry in another collection · 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 P25006
- Elsewhere: RCSB PDB 6KNG · PDBe 6KNG · UniProt P25006
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