MolNFT v1 · #151034 · protein
Cu-containing nitrite reductase (nirk) from thermus scotoductus sa-01
6HBE · Copper-containing nitrite reductase: “Cu-containing nitrite reductase (nirk) from thermus scotoductus sa-01”. X-ray diffraction, 2 ligands (CU, CA), 13 pockets (best druggability 0.81). MolNFT v1 #151034 on GenesisL1: 3D structure…
- PDB
- 6HBE
- Type
- protein
- Length
- 1,277 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- UniProt
- E8PLV7
- Ligands
- CU, CA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Copper-containing nitrite reductase | protein | 425 | 10% helix, 44% strand | E8PLV7 |
| C | Copper-containing nitrite reductase | protein | 427 | 10% helix, 44% strand | E8PLV7 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 9 copies · chains A, C, B
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.81 | 0.90 | 47 | empty |
| 2 | 300 | 0.77 | 0.88 | 23 | empty |
| 3 | 322 | 0.68 | 0.82 | 49 | empty |
| 4 | 318 | 0.68 | 0.82 | 50 | empty |
| 5 | 220 | 0.64 | 0.83 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2554 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2528 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2518 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6HBE · Cu-containing nitrite reductase (NirK) from Thermus scotoductus SA-01 · 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 E8PLV7
- Elsewhere: RCSB PDB 6HBE · PDBe 6HBE · UniProt E8PLV7
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