MolNFT v1 · #140560 · protein + DNA
Crystal structure of ctcf ZFS6-11-GB7CSE
5YEL · DNA (26-mer): “Crystal structure of ctcf ZFS6-11-GB7CSE”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.67). MolNFT v1 #140560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YEL
- Type
- protein + DNA
- Length
- 438 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (26-mer); Transcriptional repressor ctcf
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | DNA (26-mer) | dna | 26 | — | — |
| A | Transcriptional repressor ctcf | protein | 166 | 36% helix, 13% strand | P49711 |
| B | Transcriptional repressor ctcf | protein | 168 | 36% helix, 8% strand | P49711 |
| C, E | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.67 | 0.82 | 29 | empty |
| 2 | 322 | 0.66 | 0.81 | 27 | empty |
| 3 | 507 | 0.63 | 0.76 | 33 | empty |
| 4 | 466 | 0.61 | 0.76 | 30 | empty |
| 5 | 240 | 0.57 | 0.79 | 27 | empty |
Interfaces
7 interfaces between chains.
- D–B · 1293 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–F · 1286 Ų buried · 23 hydrogen bonds · protein-nucleic
- F–E · 1116 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- D–C · 1107 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- A–E · 945 Ų buried · 18 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 5YEL · PDBe 5YEL · UniProt P49711
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