MolNFT v1 · #169866 · protein
Cryo-EM structure of human ZNT8 wt, in the absence of zinc, determined in heterogeneous conformations- one subunit in an inward-facing and the other in an outward-facing conformation
6XPF · Zinc transporter 8: “Cryo-EM structure of human ZNT8 wt, in the absence of zinc, determined in heterogeneous conformations- one…”. Electron microscopy, 1 ligand (ZN), 6 pockets (best druggability 0.58). MolNFT v1 #169866 on…
- PDB
- 6XPF
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc transporter 8
- UniProt
- Q8IWU4
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.58
Structure
electron microscopy · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc transporter 8 | protein | 291 | 62% helix, 8% strand | Q8IWU4 |
| B | Zinc transporter 8 | protein | 285 | 61% helix, 8% strand | Q8IWU4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.58 | 0.73 | 75 | ZN |
| 2 | 392 | 0.51 | 0.72 | 56 | empty |
| 3 | 304 | 0.48 | 0.73 | 52 | empty |
| 4 | 346 | 0.48 | 0.72 | 54 | empty |
| 5 | 156 | 0.37 | 0.72 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 381 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6XPF · Cryo-EM structure of human ZnT8 WT, in the absence of zinc, determined in heterogeneous… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IWU4 · AlphaFold monomer V2.0 prediction for zinc transporter 8 (Q8IWU4) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q8IWU4
- Elsewhere: RCSB PDB 6XPF · PDBe 6XPF · UniProt Q8IWU4
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