Research workbench
Structure of the RAD14 DNA-binding domain in complex with N2- acetylaminonaphtyl- guanine containing DNA
Analyse Structure of the RAD14 DNA-binding domain in complex with N2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LCM
- Type
- protein + DNA
- Length
- 257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD14; DNA (5'-D(*GP*CP*TP*CP*TP*AP*CP*(AAN)P*TP*CP*AP*TP*CP*A)- 3')…
- UniProt
- P28519
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD14 | protein | 115 | 50% helix, 10% strand | P28519 |
| B | DNA repair protein RAD14 | protein | 114 | 49% helix, 10% strand | P28519 |
| C | DNA (5'-D(*GP*CP*TP*CP*TP*AP*CP*(AAN)P*TP*CP*AP*TP*CP*A)- 3') | dna | 14 | — | — |
| D | DNA (5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*G)-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 | 989 | 0.77 | 0.79 | 50 | empty |
Interfaces
5 interfaces between chains.
- C–D · 676 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–C · 489 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 480 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 397 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 382 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5LCM · STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH N2-acetylaminonaphtyl- GUANINE… · the same entry in another collection · chain A against A, 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 5LCM · PDBe 5LCM · UniProt P28519
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