MolNFT v1 · #125647 · protein
Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase phrb - Y424F mutant with impaired DNA repair activity
5LFA: “Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase phrb - Y424F mutant with…”. X-ray diffraction, 3 ligands (FAD, DLZ, SF4), 5 pockets (best druggability 0.82). MolNFT v1 #125647 on GenesisL1: 3D…
- PDB
- 5LFA
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (6-4) photolyase
- EC
- 4.1.99.13
- UniProt
- A9CH39
- Ligands
- FAD, DLZ, SF4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (6-4) photolyase (EC 4.1.99.13) | protein | 500 | 54% helix, 7% strand | A9CH39 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- DLZ · 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.82 | 0.99 | 25 | DLZ |
| 2 | 612 | 0.81 | 0.86 | 68 | FAD |
| 3 | 183 | 0.62 | 0.83 | 25 | empty |
| 4 | 72 | 0.40 | 0.79 | 21 | empty |
| 5 | 52 | 0.31 | 0.77 | 14 | empty |
Compared structures
- 5LFA · Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase PhrB… · the same entry in another collection · chain A against A, TM-score 1.00
- A9CH39 · AlphaFold monomer V2.0 prediction for (6-4) photolyase (A9CH39) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A9CH39
- Elsewhere: RCSB PDB 5LFA · PDBe 5LFA · UniProt A9CH39
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