Research workbench
HIC2 zinc finger domain in complex with the DNA binding motif-2 of the BCL11A enhancer
Analyse HIC2 zinc finger domain in complex with the DNA binding motif-2 of the BCL11A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TXC
- Type
- protein + DNA
- Length
- 116 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*GP*AP*TP*AP*AP*TP*GP*CP*CP*AP*AP*CP*AP*GP*T)- 3'); DNA…
- UniProt
- Q96JB3
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*AP*GP*AP*TP*AP*AP*TP*GP*CP*CP*AP*AP*CP*AP*GP*T)- 3') | dna | 16 | — | — |
| B | DNA (5'-D(*AP*CP*TP*GP*TP*TP*GP*GP*CP*AP*TP*TP*AP*TP*CP*T)- 3') | dna | 16 | — | — |
| E | Hypermethylated in cancer 2 protein | protein | 84 | 40% helix, 14% strand | Q96JB3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.55 | 0.78 | 23 | empty |
| 2 | 50 | 0.53 | 0.89 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 704 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- B–E · 684 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–E · 501 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7TXC · HIC2 zinc finger domain in complex with the DNA binding motif-2 of the BCL11A enhancer · the same entry in another collection · chain A against A, TM-score 1.00
- Q96JB3 · AlphaFold monomer V2.0 prediction for hypermethylated in cancer 2 protein (Q96JB3) · a predicted model of the same protein · chain E against A, TM-score 0.57
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 Q96JB3
- Elsewhere: RCSB PDB 7TXC · PDBe 7TXC · UniProt Q96JB3
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