MolNFT v1 · #140554 · protein + DNA
Crystal structure of ctcf ZFS2-8-HS5-1AE
5YEF · Transcriptional repressor ctcf: “Crystal structure of ctcf ZFS2-8-HS5-1AE”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.62). MolNFT v1 #140554 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YEF
- Type
- protein + DNA
- Length
- 888 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor ctcf; DNA (27-mer)
- UniProt
- P49711
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Transcriptional repressor ctcf | protein | 169 | 38% helix, 15% strand | P49711 |
| C, E, H, K | DNA (27-mer) | dna | 27 | — | — |
| D, F, I, L | DNA (27-mer) | dna | 27 | — | — |
| B, J | Transcriptional repressor ctcf | protein | 167 | 36% helix, 11% strand | P49711 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.62 | 0.82 | 34 | empty |
| 2 | 217 | 0.60 | 0.81 | 27 | empty |
| 3 | 333 | 0.59 | 0.77 | 28 | empty |
| 4 | 162 | 0.59 | 0.83 | 21 | empty |
| 5 | 150 | 0.59 | 0.84 | 20 | empty |
Interfaces
16 interfaces between chains.
- A–D · 1512 Ų buried · 36 hydrogen bonds · protein-nucleic
- G–I · 1509 Ų buried · 39 hydrogen bonds · protein-nucleic
- B–F · 1496 Ų buried · 43 hydrogen bonds · protein-nucleic
- J–L · 1475 Ų buried · 40 hydrogen bonds · protein-nucleic
- K–L · 1231 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Compared structures
- 5YEF · Crystal structure of CTCF ZFs2-8-Hs5-1aE · the same entry in another collection · chain K against K, TM-score 1.00
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 5YEF · PDBe 5YEF · UniProt P49711
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