MolNFT v1 · #66310 · protein
Crystal structure of pqqc active site mutant H154S in complex with pqq
3HML · Pyrroloquinoline-quinone synthase: “Crystal structure of pqqc active site mutant H154S in complex with pqq”. X-ray diffraction, 1 ligand (PQQ), 7 pockets (best druggability 0.76). MolNFT v1 #66310 on GenesisL1: 3D structure, binding…
- 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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