MolNFT v1 · #119663 · protein + DNA
Structure of RAD14 in complex with acetylnaphtyl-guanine containing DNA
5G33: “Structure of RAD14 in complex with acetylnaphtyl-guanine containing DNA”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.73). MolNFT v1 #119663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G33
- Type
- protein + DNA
- Length
- 285 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAD14; 5'-D(*GP*CP*TP*CP*TP*AP*MFOP*TP*CP*AP*TP*CP*AP*CP)-3'…
- UniProt
- P28519
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAD14 | protein | 114 | 49% helix, 11% strand | P28519 |
| B | RAD14 | protein | 115 | 50% helix, 10% strand | P28519 |
| C, E | 5'-D(*GP*CP*TP*CP*TP*AP*MFOP*TP*CP*AP*TP*CP*AP*CP)-3' | dna | 14 | — | — |
| D, F | 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3' | dna | 14 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.73 | 0.79 | 80 | empty |
Interfaces
14 interfaces between chains.
- D–E · 1686 Ų buried · 523 hydrogen bonds · nucleic-nucleic
- C–F · 1677 Ų buried · 529 hydrogen bonds · nucleic-nucleic
- E–F · 660 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- C–E · 659 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- C–D · 638 Ų buried · 57 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5G33 · Structure of Rad14 in complex with acetylnaphtyl-guanine containing DNA · the same entry in another collection · chain F against F, TM-score 1.00
- P28519 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD14 (P28519) · a predicted model of the same protein · chain A 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 P28519
- Elsewhere: RCSB PDB 5G33 · PDBe 5G33 · UniProt P28519
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