MolNFT v1 · #124350 · protein
Crystal structure of iron-sulfur cluster containing photolyase phrb mutant I51W
5KCM · (6-4) photolyase: “Crystal structure of iron-sulfur cluster containing photolyase phrb mutant I51W”. X-ray diffraction, 2 ligands (FAD, SF4), 14 pockets (best druggability 0.83). MolNFT v1 #124350 on GenesisL1: 3D structure, binding…
- PDB
- 5KCM
- Type
- protein
- Length
- 1,024 residues
- Chains
- 2
- 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, SF4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | (6-4) photolyase (EC 4.1.99.13) | protein | 512 | 52% helix, 7% strand | A9CH39 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.83 | 0.87 | 61 | FAD |
| 2 | 826 | 0.82 | 0.85 | 71 | FAD, GOL |
| 3 | 388 | 0.80 | 0.89 | 52 | GOL |
| 4 | 232 | 0.79 | 0.92 | 28 | GOL |
| 5 | 778 | 0.76 | 0.80 | 73 | empty |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5KCM · Crystal structure of iron-sulfur cluster containing photolyase PhrB mutant I51W · 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 5KCM · PDBe 5KCM · UniProt A9CH39
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