MolNFT v1 · #105726 · protein
Structure of the bacterial zn-transporter znud from neisseria meningitidis (locked conformation bound to zinc and cadmium ions)
4RDR: “Structure of the bacterial zn-transporter znud from neisseria meningitidis (locked conformation bound to zinc…”. X-ray diffraction, 3 ligands (CD, ZN, SO4), 8 pockets (best druggability 0.88). MolNFT v1 #105726 on GenesisL1: 3D…
- PDB
- 4RDR
- Type
- protein
- Length
- 706 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Znud
- UniProt
- Q9JZN9
- Ligands
- CD, ZN, SO4
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Znud | protein | 706 | 8% helix, 54% strand | Q9JZN9 |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 21 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.88 | 0.89 | 109 | SO4 |
| 2 | 1032 | 0.85 | 0.86 | 113 | SO4 |
| 3 | 152 | 0.64 | 0.86 | 30 | empty |
| 4 | 160 | 0.53 | 0.80 | 25 | empty |
| 5 | 132 | 0.49 | 0.79 | 29 | empty |
Modifications
Observed in the structure: 7 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 4RDR · Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JZN9 · AlphaFold monomer V2.0 prediction for probable tonb-dependent receptor NMB0964 (Q9JZN9) · 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 Q9JZN9
- Elsewhere: RCSB PDB 4RDR · PDBe 4RDR · UniProt Q9JZN9
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