MolNFT v1 · #11616 · protein
Crystal structure of ARG402ALA mutant flavocytochrome C3 from shewanella frigidimarina
1JRX: “Crystal structure of ARG402ALA mutant flavocytochrome C3 from shewanella frigidimarina”. X-ray diffraction, 4 ligands (HEM, FAD, FUM), 9 pockets (best druggability 0.87). MolNFT v1 #11616 on GenesisL1: 3D structure, binding sites…
- PDB
- 1JRX
- Type
- protein
- Length
- 1,136 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavocytochrome C
- EC
- 1.3.99.1
- UniProt
- Q02469
- Ligands
- HEM, FAD, FUM, NA
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Flavocytochrome C (EC 1.3.99.1) | protein | 568 | 36% helix, 18% strand | Q02469 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- FUM · Fumaric acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 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 | 988 | 0.87 | 0.88 | 148 | HEM, FAD, FUM |
| 2 | 1006 | 0.87 | 0.88 | 145 | HEM, FAD, FUM |
| 3 | 893 | 0.74 | 0.78 | 94 | empty |
| 4 | 202 | 0.63 | 0.83 | 28 | empty |
| 5 | 204 | 0.63 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1JRX · Crystal structure of Arg402Ala mutant flavocytochrome c3 from Shewanella frigidimarina · 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 Q02469
- Elsewhere: RCSB PDB 1JRX · PDBe 1JRX · UniProt Q02469
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