Research workbench
Homo sapiens ccctc-binding factor (ctcf) ZNF5-8 and DNA complex structure in space group P41212
Analyse Homo sapiens ccctc-binding factor (ctcf) ZNF5-8 and DNA complex structure in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K5J
- Type
- protein + DNA
- Length
- 140 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor ctcf; DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*AP*C)-3')…
- UniProt
- P49711
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional repressor ctcf | protein | 114 | 39% helix, 14% strand | P49711 |
| B | DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*AP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*TP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- SO4 · Sulfate ion · ion · chains A, B
- ACT · Acetate ion · additive · chains A, C
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 | 171 | 0.54 | 0.80 | 23 | empty |
| 2 | 77 | 0.34 | 0.76 | 13 | empty |
| 3 | 65 | 0.28 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 924 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 574 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–B · 405 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5K5J · Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group… · the same entry in another collection · chain A against A, TM-score 1.00
- P49711 · AlphaFold monomer V2.0 prediction for transcriptional repressor ctcf (P49711) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 P49711
- Elsewhere: RCSB PDB 5K5J · PDBe 5K5J · UniProt P49711
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