Research workbench
Crystal structure of pfad from shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.
Analyse Crystal structure of pfad from shewanella oneidensis in complex with NAD+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z9R
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omega-3 polyunsaturated fatty acid synthase subunit pfad
- UniProt
- Q8EGK4
- Ligands
- NAD, FMN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Omega-3 polyunsaturated fatty acid synthase subunit pfad | protein | 495 | 45% helix, 14% strand | Q8EGK4 |
| B | Omega-3 polyunsaturated fatty acid synthase subunit pfad | protein | 501 | 47% helix, 13% strand | Q8EGK4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.81 | 0.85 | 88 | empty |
| 2 | 950 | 0.78 | 0.81 | 74 | NAD, FMN |
| 3 | 854 | 0.78 | 0.81 | 89 | NAD, FMN |
| 4 | 122 | 0.52 | 0.81 | 18 | empty |
| 5 | 175 | 0.52 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1599 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4Z9R · Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by… · 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 Q8EGK4
- Elsewhere: RCSB PDB 4Z9R · PDBe 4Z9R · UniProt Q8EGK4
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