MolNFT v1 · #140555 · protein + DNA
Crystal structure of ctcf ZFS4-8-HS5-1A complex
5YEG · Transcriptional repressor ctcf: “Crystal structure of ctcf ZFS4-8-HS5-1A complex”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.62). MolNFT v1 #140555 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5YEG
- Type
- protein + DNA
- Length
- 359 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor ctcf; DNA (5'- D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*T…
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional repressor ctcf | protein | 138 | 39% helix, 14% strand | P49711 |
| B | Transcriptional repressor ctcf | protein | 141 | 39% helix, 14% strand | P49711 |
| D, E | DNA (5'- D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3') | dna | 20 | — | — |
| C, F | DNA (5'- D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3') | dna | 20 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.62 | 0.81 | 31 | empty |
| 2 | 357 | 0.56 | 0.75 | 27 | empty |
| 3 | 351 | 0.55 | 0.75 | 24 | empty |
| 4 | 145 | 0.52 | 0.80 | 20 | empty |
| 5 | 75 | 0.50 | 0.84 | 14 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1264 Ų buried · 36 hydrogen bonds · protein-nucleic
- B–F · 1236 Ų buried · 34 hydrogen bonds · protein-nucleic
- D–C · 896 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- E–F · 892 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- B–E · 690 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
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 5YEG · PDBe 5YEG · UniProt P49711
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