Research workbench
Bond length analysis of the pqqc Y175F mutant structure shows evidence for bound pqq in the reduced form
Analyse Bond length analysis of the pqqc Y175F mutant structure shows evidence for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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