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(6-4) photolyase crystal structure

Analyse (6-4) photolyase crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FY4
Type: protein
Length: 1,563 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-4 photolyase
UniProt: O48652
Ligands: FAD, PO4
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-4 photolyase	protein	522	46% helix, 6% strand	O48652
B	6-4 photolyase	protein	521	47% helix, 6% strand	O48652
C	6-4 photolyase	protein	520	48% helix, 6% strand	O48652

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, C, B
PO4 · Phosphate ion · ion · 3 copies · chains A, C, B
IMD · Imidazole · additive · 10 copies · chains A, C, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, C, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	755	0.84	0.87	71	IMD, MES, FAD
2	1113	0.83	0.84	102	IMD, MES, FAD
3	485	0.82	0.88	45	IMD, MES, FAD
4	287	0.82	0.92	29	empty
5	314	0.81	0.91	33	empty

Interfaces

2 interfaces between chains.

A–C · 631 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 604 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3FY4 · (6-4) Photolyase Crystal Structure · the same entry in another collection · chain A against A, TM-score 1.00
O48652 · AlphaFold monomer V2.0 prediction for (6-4)DNA photolyase (O48652) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 O48652
Elsewhere: RCSB PDB 3FY4 · PDBe 3FY4 · UniProt O48652

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