MolNFT v1 · #153406 · protein
Crystal structure of a DNA repair protein
6JDE · Putative DNA repair helicase radd: “Crystal structure of a DNA repair protein”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.77). MolNFT v1 #153406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JDE
- Type
- protein
- Length
- 1,127 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
- ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Putative DNA repair helicase radd (EC 3.6.4.12) | protein | 567 | 26% helix, 27% strand | P33919 |
| A | Putative DNA repair helicase radd (EC 3.6.4.12) | protein | 560 | 27% helix, 26% strand | P33919 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.77 | 0.83 | 71 | empty |
| 2 | 363 | 0.69 | 0.82 | 37 | empty |
| 3 | 87 | 0.66 | 0.91 | 23 | empty |
| 4 | 250 | 0.64 | 0.82 | 44 | empty |
| 5 | 392 | 0.61 | 0.77 | 34 | empty |
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 6JDE · PDBe 6JDE · UniProt P33919
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