Research workbench
Crystal structure of C-terminal desundecapeptide nitrite reductase from achromobacter cycloclastes
Analyse Crystal structure of C-terminal desundecapeptide nitrite reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AVF
- Type
- protein
- Length
- 1,904 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- P25006
- Ligands
- CU, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 314 | 8% helix, 43% strand | P25006 |
| B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 316 | 9% helix, 43% strand | P25006 |
| C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 316 | 9% helix, 41% strand | P25006 |
| D | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 320 | 9% helix, 43% strand | P25006 |
| E | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 315 | 7% helix, 43% strand | P25006 |
| F | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 323 | 9% helix, 42% strand | P25006 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.83 | 0.95 | 27 | empty |
| 2 | 257 | 0.82 | 0.95 | 29 | empty |
| 3 | 576 | 0.82 | 0.87 | 52 | empty |
| 4 | 590 | 0.81 | 0.86 | 51 | empty |
| 5 | 107 | 0.78 | 0.97 | 19 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1495 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1426 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1422 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1407 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1364 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2AVF · Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter… · the same entry in another collection · chain F against F, TM-score 1.00
- P25006 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P25006) · a predicted model of the same protein · chain C 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 2AVF · PDBe 2AVF · UniProt P25006
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