Research workbench
NMR structure of E. COLI ada protein in complex with DNA
Analyse NMR structure of E. COLI ada protein in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZGW
- Type
- protein + DNA
- Length
- 175 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*AP*AP*AP*TP*TP*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*A) -3'…
- UniProt
- P06134
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.64
Structure
solution nmr · 3 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*CP*AP*AP*AP*TP*TP*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*A) -3' | dna | 18 | — | — |
| C | 5'-D(*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*TP*AP*AP*TP*TP*TP*GP*C) -3' | dna | 18 | — | — |
| A | Ada polyprotein | protein | 139 | 46% 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 | 517 | 0.64 | 0.76 | 53 | empty |
| 2 | 54 | 0.33 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 842 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- C–A · 760 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–A · 500 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 1ZGW · NMR structure of E. Coli Ada protein in complex with DNA · 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 0.61
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 1ZGW · PDBe 1ZGW · UniProt P06134
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