MolNFT v1 · #124109 · protein + DNA
Homo sapiens ccctc-binding factor (ctcf) ZNF6-8 and H19 sequence DNA complex structure
5K5L · DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3'): “Homo sapiens ccctc-binding factor (ctcf) ZNF6-8 and H19 sequence DNA complex structure”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.70). MolNFT v1 #124109 on…
- PDB
- 5K5L
- Type
- protein + DNA
- Length
- 239 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3'); DNA…
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3') | dna | 10 | — | — |
| B | DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3') | dna | 11 | — | — |
| D | DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3') | dna | 11 | — | — |
| E | Transcriptional repressor ctcf | protein | 56 | 43% helix, 14% strand | P49711 |
| F | Transcriptional repressor ctcf | protein | 57 | 39% helix, 23% strand | P49711 |
| G | Transcriptional repressor ctcf | protein | 84 | 40% helix, 10% strand | P49711 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.70 | 0.79 | 46 | empty |
| 2 | 289 | 0.57 | 0.77 | 25 | empty |
| 3 | 321 | 0.55 | 0.76 | 30 | empty |
| 4 | 137 | 0.47 | 0.78 | 15 | empty |
| 5 | 125 | 0.43 | 0.77 | 17 | empty |
Interfaces
16 interfaces between chains.
- C–D · 518 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–B · 450 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- C–F · 367 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–E · 339 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–G · 314 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5K5L · Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure · the same entry in another collection · chain G against G, TM-score 1.00
- P49711 · AlphaFold monomer V2.0 prediction for transcriptional repressor ctcf (P49711) · a predicted model of the same protein · chain E against A, TM-score 0.95
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 5K5L · PDBe 5K5L · UniProt P49711
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