Research workbench
Crystal structure of the methylated N-ADA/DNA complex
Analyse Crystal structure of the methylated N-ADA/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U8B
- Type
- protein + DNA
- Length
- 166 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*AP*AP*AP*TP*T)-3'; 5'-D(P*AP*AP*TP*TP*T)-3'…
- UniProt
- P06134
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*TP*AP*AP*AP*TP*T)-3' | dna | 5 | — | — |
| C | 5'-D(P*AP*AP*TP*TP*T)-3' | dna | 5 | — | — |
| D | 5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3' | dna | 12 | — | — |
| E | 5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3' | dna | 12 | — | — |
| A | Ada polyprotein | protein | 132 | 49% helix, 11% strand | P06134 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.55 | 0.75 | 24 | empty |
| 2 | 115 | 0.37 | 0.74 | 16 | empty |
Interfaces
10 interfaces between chains.
- D–E · 543 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- B–A · 506 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–A · 263 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 252 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 204 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (engineered, methylation).
Compared structures
- 1U8B · Crystal structure of the methylated N-ADA/DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
- P06134 · AlphaFold monomer V2.0 prediction for bifunctional transcriptional ACTIVATOR/DNA repair… · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P06134
- Elsewhere: RCSB PDB 1U8B · PDBe 1U8B · UniProt P06134
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