Research workbench
X-ray structure of the metal-sensor cnrx in both the apo- and copper- bound forms
Analyse X-ray structure of the metal-sensor cnrx in both the apo- and copper- bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EPV
- Type
- protein
- Length
- 433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel and cobalt resistance protein cnrr
- UniProt
- P37975
- Ligands
- CU
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Nickel and cobalt resistance protein cnrr | protein | 109 | 85% helix, 0% strand | P37975 |
| C | Nickel and cobalt resistance protein cnrr | protein | 106 | 87% helix, 0% strand | P37975 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.70 | 0.76 | 75 | empty |
| 2 | 309 | 0.57 | 0.76 | 41 | empty |
| 3 | 113 | 0.37 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1557 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1457 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 118 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 104 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3EPV · X-ray Structure of the Metal-sensor CnrX in both the Apo- and Copper-bound Forms · the same entry in another collection · chain D against D, TM-score 1.00
- P37975 · AlphaFold monomer V2.0 prediction for nickel and cobalt resistance protein cnrr (P37975) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P37975
- Elsewhere: RCSB PDB 3EPV · PDBe 3EPV · UniProt P37975
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