MolNFT v1 · #96999 · protein
X-ray crystal structure of a heavy metal efflux pump, crystal form I
4K0J · Heavy metal cation tricomponent efflux pump ZNEA(CZCA- like): “X-ray crystal structure of a heavy metal efflux pump, crystal form I”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #96999 on…
- PDB
- 4K0J
- Type
- protein
- Length
- 5,742 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy metal cation tricomponent efflux pump ZNEA(CZCA- like)
- UniProt
- Q1LCD8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Heavy metal cation tricomponent efflux pump ZNEA(CZCA- like) | protein | 958 | 47% helix, 20% strand | Q1LCD8 |
| B, E | Heavy metal cation tricomponent efflux pump ZNEA(CZCA- like) | protein | 954 | 49% helix, 19% strand | Q1LCD8 |
| C, F | Heavy metal cation tricomponent efflux pump ZNEA(CZCA- like) | protein | 959 | 47% helix, 20% strand | Q1LCD8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.86 | 0.89 | 126 | ZN |
| 2 | 409 | 0.85 | 0.93 | 69 | ZN |
| 3 | 1071 | 0.85 | 0.86 | 157 | ZN |
| 4 | 338 | 0.85 | 0.94 | 52 | empty |
| 5 | 334 | 0.84 | 0.94 | 55 | empty |
Interfaces
8 interfaces between chains.
- D–E · 2504 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2469 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2392 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 2362 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2352 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4K0J · X-ray crystal structure of a heavy metal efflux pump, crystal form I · the same entry in another collection · chain A against A, TM-score 1.00
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 Q1LCD8
- Elsewhere: RCSB PDB 4K0J · PDBe 4K0J · UniProt Q1LCD8
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