MolNFT v1 · #124105 · protein + DNA
Homo sapiens ccctc-binding factor (ctcf) ZNF4-7 and DNA complex structure
5K5H · Transcriptional repressor ctcf: “Homo sapiens ccctc-binding factor (ctcf) ZNF4-7 and DNA complex structure”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.48). MolNFT v1 #124105 on GenesisL1: 3D structure, binding…
- PDB
- 5K5H
- Type
- protein + DNA
- Length
- 137 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor ctcf; DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3')…
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional repressor ctcf | protein | 111 | 37% helix, 9% strand | P49711 |
| B | DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.48 | 0.79 | 18 | empty |
| 2 | 67 | 0.40 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 979 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 756 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 598 Ų buried · 72 hydrogen bonds · nucleic-nucleic
Compared structures
- 5K5H · Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure · 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 0.88
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 5K5H · PDBe 5K5H · UniProt P49711
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