MolNFT v1 · #23528 · protein
Crystal structure of the staphylococcus aureus PI258 cadc
1U2W · Cadmium efflux system accessory protein: “Crystal structure of the staphylococcus aureus PI258 cadc”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.51). MolNFT v1 #23528 on GenesisL1: 3D structure, binding sites…
- PDB
- 1U2W
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadmium efflux system accessory protein
- UniProt
- P20047
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadmium efflux system accessory protein | protein | 105 | 68% helix, 9% strand | P20047 |
| B | Cadmium efflux system accessory protein | protein | 107 | 64% helix, 11% strand | P20047 |
| C | Cadmium efflux system accessory protein | protein | 98 | 63% helix, 14% strand | P20047 |
| D | Cadmium efflux system accessory protein | protein | 94 | 77% helix, 2% strand | P20047 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.51 | 0.78 | 28 | empty |
| 2 | 158 | 0.50 | 0.78 | 26 | empty |
| 3 | 81 | 0.45 | 0.80 | 17 | empty |
| 4 | 57 | 0.26 | 0.73 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2423 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2171 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 476 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 155 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1U2W · Crystal Structure of the Staphylococcus aureus pI258 CadC · the same entry in another collection · chain D against D, TM-score 1.00
- P20047 · AlphaFold monomer V2.0 prediction for cadmium resistance transcriptional regulatory… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P20047
- Elsewhere: RCSB PDB 1U2W · PDBe 1U2W · UniProt P20047
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