MolNFT v1 · #134330 · protein + DNA
Ctcf ZNF2-7 and DNA complex structure
5T0U · Transcriptional repressor ctcf: “Ctcf ZNF2-7 and DNA complex structure”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.68). MolNFT v1 #134330 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T0U
- Type
- protein + DNA
- Length
- 431 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor ctcf; DNA (5'- D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*C…
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional repressor ctcf | protein | 170 | 39% helix, 14% strand | P49711 |
| B, E | DNA (5'- D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP* C)-3') | dna | 23 | — | — |
| C, F | DNA (5'- D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*AP*GP*TP*GP*AP*GP* G)-3') | dna | 23 | — | — |
| D | Transcriptional repressor ctcf | protein | 169 | 40% helix, 13% strand | P49711 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.68 | 0.82 | 43 | empty |
| 2 | 121 | 0.63 | 0.88 | 19 | empty |
| 3 | 109 | 0.62 | 0.88 | 16 | empty |
| 4 | 107 | 0.59 | 0.86 | 20 | empty |
| 5 | 172 | 0.57 | 0.82 | 26 | empty |
Interfaces
9 interfaces between chains.
- D–F · 1778 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–C · 1747 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–B · 1072 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–F · 1064 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- B–C · 1061 Ų buried · 96 hydrogen bonds · nucleic-nucleic
Compared structures
- P49711 · AlphaFold monomer V2.0 prediction for transcriptional repressor ctcf (P49711) · a predicted model of the same protein · chain D against A, TM-score 0.73
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 5T0U · PDBe 5T0U · UniProt P49711
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