Research workbench
Se-met form of cupriavidus metallidurans CH34 cnrxs
Analyse Se-met form of cupriavidus metallidurans CH34 cnrxs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y3G
- Type
- protein
- Length
- 437 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
- ZN, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Nickel and cobalt resistance protein cnrr | protein | 109 | 85% helix, 0% strand | P37975 |
| B | Nickel and cobalt resistance protein cnrr | protein | 110 | 83% helix, 0% strand | P37975 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.70 | 0.77 | 69 | empty |
| 2 | 380 | 0.62 | 0.77 | 44 | empty |
| 3 | 59 | 0.49 | 0.85 | 14 | empty |
| 4 | 145 | 0.40 | 0.74 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1546 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1517 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 109 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 46 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 2Y3G · Se-Met form of Cupriavidus metallidurans CH34 CnrXs · 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 A 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 2Y3G · PDBe 2Y3G · UniProt P37975
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