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Hexameric structure of copper-containing nitrite reductase of an anammox organism ksu-1
Analyse Hexameric structure of copper-containing nitrite reductase of an anammox… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZL1
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative copper-type nitrite reductase
- UniProt
- I3IR93
- Ligands
- CU, CA, SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative copper-type nitrite reductase | protein | 306 | 6% helix, 46% strand | I3IR93 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 9 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.83 | 0.89 | 49 | empty |
| 2 | 319 | 0.83 | 0.93 | 40 | CU |
| 3 | 824 | 0.70 | 0.76 | 95 | empty |
| 4 | 80 | 0.34 | 0.75 | 15 | empty |
| 5 | 62 | 0.33 | 0.76 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1484 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1476 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1475 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ZL1 · Hexameric structure of copper-containing nitrite reductase of an anammox organism KSU-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 I3IR93
- Elsewhere: RCSB PDB 5ZL1 · PDBe 5ZL1 · UniProt I3IR93
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