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Crystal structure of radd with ADP
Analyse Crystal structure of radd with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R7J
- Type
- protein
- Length
- 1,146 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA repair helicase radd
- EC
- 3.6.4.12
- UniProt
- P33919
- Ligands
- ADP, ZN, MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative DNA repair helicase radd (EC 3.6.4.12) | protein | 572 | 26% helix, 27% strand | P33919 |
| B | Putative DNA repair helicase radd (EC 3.6.4.12) | protein | 574 | 25% helix, 27% strand | P33919 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.81 | 0.82 | 110 | MG |
| 2 | 917 | 0.80 | 0.82 | 105 | ADP, MG |
| 3 | 491 | 0.68 | 0.79 | 35 | empty |
| 4 | 240 | 0.66 | 0.83 | 36 | empty |
| 5 | 470 | 0.64 | 0.77 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 11 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 P33919
- Elsewhere: RCSB PDB 7R7J · PDBe 7R7J · UniProt P33919
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