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Crystal structure of dodecylphosphocholine-solubilized nccx from cupriavidus metallidurans 31A
Analyse Crystal structure of dodecylphosphocholine-solubilized nccx from cupriavidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CLV
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-cobalt-cadmium resistance protein nccx
- UniProt
- Q44582
- Ligands
- PC, ZN, PO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nickel-cobalt-cadmium resistance protein nccx | protein | 142 | 85% helix, 0% strand | Q44582 |
Ligands and binding sites
- PC · Phosphocholine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 10 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.79 | 0.83 | 53 | PO4 |
| 2 | 205 | 0.53 | 0.77 | 26 | empty |
| 3 | 163 | 0.50 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4CLV · Crystal Structure of dodecylphosphocholine-solubilized NccX from Cupriavidus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q44582 · AlphaFold monomer V2.0 prediction for nickel-cobalt-cadmium resistance protein nccx… · a predicted model of the same protein · chain A against A, TM-score 0.75
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 Q44582
- Elsewhere: RCSB PDB 4CLV · PDBe 4CLV · UniProt Q44582
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