Research workbench
Structure of deoxyribodipyrimidine photolyase
Analyse Structure of deoxyribodipyrimidine photolyase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DNP
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA photolyase
- EC
- 4.1.99.3
- UniProt
- P00914
- Ligands
- FAD, MHF
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA photolyase (EC 4.1.99.3) | protein | 469 | 52% helix, 6% strand | P00914 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MHF · 5,10-methenyl-6,7,8-trihydrofolic acid · ligand · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.83 | 0.89 | 41 | FAD |
| 2 | 534 | 0.83 | 0.89 | 39 | FAD |
| 3 | 337 | 0.79 | 0.90 | 52 | MHF |
| 4 | 338 | 0.78 | 0.88 | 51 | MHF |
| 5 | 766 | 0.71 | 0.78 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1121 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 P00914
- Elsewhere: RCSB PDB 1DNP · PDBe 1DNP · UniProt P00914
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