Research workbench
Crystal structure of pqqc active site mutant H154S in complex with pqq
Analyse Crystal structure of pqqc active site mutant H154S in complex with pqq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HML
- Type
- protein
- Length
- 473 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
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroloquinoline-quinone synthase (EC 1.3.3.11) | protein | 237 | 71% helix, 0% strand | A6T9H1 |
| B | Pyrroloquinoline-quinone synthase (EC 1.3.3.11) | protein | 236 | 69% helix, 0% strand | A6T9H1 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.76 | 0.98 | 27 | empty |
| 2 | 77 | 0.72 | 0.96 | 19 | empty |
| 3 | 587 | 0.72 | 0.79 | 41 | PQQ |
| 4 | 115 | 0.69 | 0.91 | 20 | empty |
| 5 | 518 | 0.68 | 0.78 | 40 | PQQ |
Interfaces
1 interface between chains.
- A–B · 2060 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3HML · Crystal Structure of PqqC Active Site Mutant H154S 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 0.96
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 3HML · PDBe 3HML · UniProt A6T9H1
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