Research workbench
Structure of the bacterial zn-transporter znud from neisseria meningitidis (flexible conformation bound to a zinc ion)
Analyse Structure of the bacterial zn-transporter znud from neisseria meningitidis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDT
- Type
- protein
- Length
- 1,270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Znud
- UniProt
- Q9JZN9
- Ligands
- ZN, SO4
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Znud | protein | 635 | 4% helix, 56% strand | Q9JZN9 |
| B | Znud | protein | 635 | 4% helix, 56% strand | Q9JZN9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.89 | 0.92 | 90 | empty |
| 2 | 919 | 0.88 | 0.91 | 94 | empty |
| 3 | 1090 | 0.83 | 0.84 | 117 | empty |
| 4 | 1125 | 0.83 | 0.84 | 127 | GOL |
| 5 | 131 | 0.58 | 0.85 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 487 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4RDT · Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (flexible… · 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 0.97
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 4RDT · PDBe 4RDT · UniProt Q9JZN9
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