Research workbench
Homo sapiens ccctc-binding factor (ctcf) ZNF3-7 and DNA complex structure
Analyse Homo sapiens ccctc-binding factor (ctcf) ZNF3-7 and DNA complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KKQ
- Type
- protein + DNA
- Length
- 360 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor ctcf; DNA (5'- D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G…
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional repressor ctcf | protein | 147 | 40% helix, 15% strand | P49711 |
| B, E | DNA (5'- D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3') | dna | 17 | — | — |
| C, F | DNA (5'- D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3') | dna | 17 | — | — |
| D | Transcriptional repressor ctcf | protein | 145 | 41% helix, 14% strand | P49711 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.62 | 0.88 | 18 | empty |
| 2 | 71 | 0.59 | 0.90 | 17 | empty |
| 3 | 114 | 0.59 | 0.86 | 18 | empty |
| 4 | 77 | 0.55 | 0.87 | 18 | empty |
| 5 | 175 | 0.52 | 0.79 | 26 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1502 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–C · 1497 Ų buried · 40 hydrogen bonds · protein-nucleic
- D–E · 897 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 891 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–F · 784 Ų buried · 68 hydrogen bonds · nucleic-nucleic
Compared structures
- 5KKQ · Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure · the same entry in another collection · chain F against F, 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 0.79
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 5KKQ · PDBe 5KKQ · UniProt P49711
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