Research workbench
Pseudomonas putida pqqb with a non-physiological zinc at the active site binds the substrate mimic, 5-cysteinyl-3,4- dihydroxyphenylalanine (5-cys-dopa), non-specifically but supports the proposed function of the enzyme in pyrroloquinoline quinone biosynthesis.
Analyse Pseudomonas putida pqqb with a non-physiological zinc at the active site binds… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E13
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme pqq synthesis protein B
- EC
- 1.-.-.-
- UniProt
- Q88QV5
- Ligands
- HKS, ZN, CL
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme pqq synthesis protein B (EC 1.-.-.-) | protein | 308 | 24% helix, 24% strand | Q88QV5 |
Ligands and binding sites
- HKS · 3-{[(2S)-2-amino-2-carboxyethyl]sulfanyl}-5-hydroxy-L-tyrosine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.60 | 0.78 | 46 | CL, HKS |
| 2 | 113 | 0.40 | 0.75 | 16 | empty |
Compared structures
- 6E13 · Pseudomonas putida PqqB with a non-physiological zinc at the active site binds the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q88QV5 · AlphaFold monomer V2.0 prediction for coenzyme pqq synthesis protein B (Q88QV5) · 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 Q88QV5
- Elsewhere: RCSB PDB 6E13 · PDBe 6E13 · UniProt Q88QV5
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