Research workbench
Homo sapiens ccctc-binding factor (ctcf) ZNF5-8 and DNA complex structure in space group P65
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
- 5K5I
- Type
- protein + DNA
- Length
- 139 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*CP*C)-3')…
- UniProt
- P49711
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional repressor ctcf | protein | 113 | 38% helix, 14% strand | P49711 |
| B | DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*CP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*GP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
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 | 189 | 0.55 | 0.80 | 33 | SO4 |
| 2 | 83 | 0.35 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 952 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 558 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–B · 431 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5K5I · 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 5K5I · PDBe 5K5I · UniProt P49711
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