MolNFT v1 · #66288 · protein
Crystal structure of pqqc active site mutant Y175F in complex with pqq
3HLX · Pyrroloquinoline-quinone synthase: “Crystal structure of pqqc active site mutant Y175F in complex with pqq”. X-ray diffraction, 2 ligands (PQQ, CL), 9 pockets (best druggability 0.81). MolNFT v1 #66288 on GenesisL1: 3D structure…
- PDB
- 3HLX
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrroloquinoline-quinone synthase
- EC
- 1.3.3.11
- UniProt
- A6T9H1
- Ligands
- PQQ, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyrroloquinoline-quinone synthase (EC 1.3.3.11) | protein | 254 | 72% helix, 0% strand | A6T9H1 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 copies · chains A, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.81 | 0.98 | 33 | PQQ, CL |
| 2 | 123 | 0.79 | 0.98 | 25 | PQQ, CL |
| 3 | 92 | 0.78 | 0.99 | 30 | empty |
| 4 | 101 | 0.74 | 0.95 | 18 | empty |
| 5 | 110 | 0.74 | 0.94 | 21 | empty |
Interfaces
1 interface between chains.
- A–D · 2279 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3HLX · Crystal Structure of PqqC Active Site Mutant Y175F in Complex with PQQ · the same entry in another collection · chain A against A, TM-score 1.00
- A6T9H1 · AlphaFold monomer V2.0 prediction for pyrroloquinoline-quinone synthase (A6T9H1) · 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 A6T9H1
- Elsewhere: RCSB PDB 3HLX · PDBe 3HLX · UniProt A6T9H1
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