MolNFT v1 · #112001 · protein
The 1.98-ångström crystal structure of ZN(2+)-bound pqqb from methylobacterium extorquens
4Z7R · Coenzyme pqq synthesis protein B: “The 1.98-ångström crystal structure of ZN(2+)-bound pqqb from methylobacterium extorquens”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.78). MolNFT v1 #112001 on GenesisL1: 3D…
- PDB
- 4Z7R
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme pqq synthesis protein B
- UniProt
- Q49149
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme pqq synthesis protein B | protein | 299 | 24% helix, 27% strand | Q49149 |
| B | Coenzyme pqq synthesis protein B | protein | 279 | 25% helix, 28% strand | Q49149 |
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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.78 | 0.87 | 54 | ZN |
| 2 | 394 | 0.60 | 0.76 | 44 | ZN |
| 3 | 63 | 0.29 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2160 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4Z7R · The 1.98-angstrom crystal structure of Zn(2+)-bound PqqB from Methylobacterium extorquens · the same entry in another collection · chain A against A, TM-score 1.00
- Q49149 · AlphaFold monomer V2.0 prediction for coenzyme pqq synthesis protein B (Q49149) · a predicted model of the same protein · chain A 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 Q49149
- Elsewhere: RCSB PDB 4Z7R · PDBe 4Z7R · UniProt Q49149
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