Research workbench
Solution NMR structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA
Analyse Solution NMR structure of kaiso zinc finger DNA binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LT7
- Type
- protein + DNA
- Length
- 171 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator kaiso; DNA (5'- D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*…
- UniProt
- Q86T24
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.78
Structure
solution nmr · 3 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator kaiso | protein | 133 | 30% helix, 20% strand | Q86T24 |
| D | DNA (5'- D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3') | dna | 19 | — | — |
| E | DNA (5'- D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3') | dna | 19 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.78 | 0.97 | 20 | empty |
| 2 | 251 | 0.50 | 0.75 | 32 | empty |
| 3 | 159 | 0.44 | 0.75 | 23 | empty |
| 4 | 145 | 0.42 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1051 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–D · 1010 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–E · 843 Ų buried · 74 hydrogen bonds · nucleic-nucleic
Compared structures
- 2LT7 · Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86T24 · AlphaFold monomer V2.0 prediction for transcriptional regulator kaiso (Q86T24) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q86T24
- Elsewhere: RCSB PDB 2LT7 · PDBe 2LT7 · UniProt Q86T24
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