MolNFT v1 · #107294 · protein
Crystal structure of a bacterial class III photolyase from agrobacterium tumefaciens at 1.67A resolution
4U63 · DNA photolyase: “Crystal structure of a bacterial class III photolyase from agrobacterium tumefaciens at 1.67A resolution”. X-ray diffraction, 3 ligands (MHF, FAD, SO4), 4 pockets (best druggability 0.82). MolNFT v1 #107294 on…
- PDB
- 4U63
- Type
- protein
- Length
- 482 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA photolyase
- UniProt
- A9CJC9
- Ligands
- MHF, FAD, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA photolyase | protein | 482 | 48% helix, 6% strand | A9CJC9 |
Ligands and binding sites
- MHF · 5,10-methenyl-6,7,8-trihydrofolic acid · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 14 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.82 | 0.85 | 71 | FAD, SO4 |
| 2 | 222 | 0.61 | 0.81 | 46 | empty |
| 3 | 120 | 0.42 | 0.76 | 22 | empty |
| 4 | 62 | 0.33 | 0.76 | 18 | empty |
Compared structures
- 4U63 · Crystal structure of a bacterial class III photolyase from Agrobacterium tumefaciens at… · the same entry in another collection · chain A against A, TM-score 1.00
- A9CJC9 · AlphaFold monomer V2.0 prediction for deoxyribodipyrimidine photo- lyase (A9CJC9) · 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 A9CJC9
- Elsewhere: RCSB PDB 4U63 · PDBe 4U63 · UniProt A9CJC9
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