MolNFT v1 · #119809 · protein + DNA
Solution NMR structure of the wild type DNA binding domain of area complexed to a 13BP DNA containing a cgata site, 35 structures
5GAT · DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3'): “Solution NMR structure of the wild type DNA binding domain of area complexed to a 13BP DNA containing a cgata…”. Solution nmr, 1 ligand (ZN), 3 pockets (best druggability…
- PDB
- 5GAT
- Type
- protein + DNA
- Length
- 92 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3'); DNA…
- UniProt
- P17429
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.66
Structure
solution nmr · 3 distinct chains · 18% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3') | dna | 13 | — | — |
| A | Nitrogen regulatory protein area | protein | 66 | 18% helix, 9% strand | P17429 |
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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.66 | 0.81 | 30 | empty |
| 2 | 137 | 0.40 | 0.75 | 14 | empty |
| 3 | 63 | 0.38 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 628 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- C–A · 574 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–A · 333 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 5GAT · Solution NMR structure of the wild type DNA binding domain of area complexed to a 13BP… · the same entry in another collection · chain C against C, TM-score 1.00
- P17429 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein area (P17429) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 P17429
- Elsewhere: RCSB PDB 5GAT · PDBe 5GAT · UniProt P17429
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