MolNFT v1 · #101660 · protein
Bond length analysis of the pqqc Y175F mutant structure shows evidence for bound pqq in the reduced form
4NY7 · Pyrroloquinoline-quinone synthase: “Bond length analysis of the pqqc Y175F mutant structure shows evidence for bound pqq in the reduced form”. X-ray diffraction, 2 ligands (PQQ, CL), 7 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 4NY7
- 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
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 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, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.80 | 0.94 | 35 | empty |
| 2 | 118 | 0.79 | 0.98 | 25 | PQQ, CL |
| 3 | 108 | 0.78 | 0.98 | 25 | PQQ, CL |
| 4 | 76 | 0.76 | 0.99 | 30 | empty |
| 5 | 98 | 0.36 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2227 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4NY7 · Bond length analysis of the PqqC Y175F mutant structure shows evidence for bound PQQ in… · 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 4NY7 · PDBe 4NY7 · UniProt A6T9H1
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