Research workbench
Crystal structure of PfaD from Shewanella piezotolerans in complex with FMN
Analyse Crystal structure of PfaD from Shewanella piezotolerans in complex with FMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKC
- Type
- protein
- Length
- 1,063 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.998
- Source
- Shewanella piezotolerans (strain WP3 / JCM 13877)
- Molecule
- Polyunsaturated fatty acid synthase PfaD
- EC
- 1.3.1.9
- UniProt
- B8CQB6
- Ligands
- FMN, CA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.998 · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyunsaturated fatty acid synthase PfaD (EC 1.3.1.9) | protein | 530 | 48% helix, 15% strand | B8CQB6 |
| B | Polyunsaturated fatty acid synthase PfaD (EC 1.3.1.9) | protein | 533 | 46% helix, 14% strand | B8CQB6 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 497 | 0.81 | 0.88 | 72 | GOL |
| 2 | 1155 | 0.78 | 0.80 | 91 | FMN, CA |
| 3 | 1129 | 0.77 | 0.79 | 97 | FMN, CA |
| 4 | 619 | 0.75 | 0.82 | 63 | GOL |
| 5 | 688 | 0.67 | 0.75 | 74 | empty |
Interfaces
1 interface between chains.
- A–B · 2088 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6LKC · Crystal structure of pfad from shewanella piezotolerans in complex with FMN · the same entry in another collection · chain A against A, TM-score 1.00
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 B8CQB6
- Elsewhere: RCSB PDB 6LKC · PDBe 6LKC · UniProt B8CQB6
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