MolNFT v1 · #140556 · protein + DNA

Crystal structure of ctcf ZFS4-8-ecbs

5YEH · Transcriptional repressor ctcf: “Crystal structure of ctcf ZFS4-8-ecbs”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.77). MolNFT v1 #140556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YEH
Type: protein + DNA
Length: 358 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional repressor ctcf; DNA (5'- D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*G…
UniProt: P49711
Ligands: ZN
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Transcriptional repressor ctcf	protein	139	39% helix, 14% strand	P49711
C, E	DNA (5'- D(APCPGPGPTPTPTPCPCPGPCPTPAPGPAPGPGPGPCPG)-3')	dna	20	—	—
D, F	DNA (5'- D(TPCPGPCPCPCPTPCPTPAPGPCPGPGPAPAPAPCPCPG)-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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	690	0.77	0.82	78	empty
2	114	0.50	0.81	22	empty
3	211	0.45	0.74	20	empty
4	75	0.44	0.81	17	empty
5	78	0.44	0.81	16	empty

Interfaces

9 interfaces between chains.

B–E · 1224 Å² buried · 30 hydrogen bonds · protein-nucleic
A–C · 1206 Å² buried · 29 hydrogen bonds · protein-nucleic
C–D · 918 Å² buried · 73 hydrogen bonds · nucleic-nucleic
E–F · 904 Å² buried · 70 hydrogen bonds · nucleic-nucleic
A–D · 661 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

5YEH · Crystal structure of CTCF ZFs4-8-eCBS · the same entry in another collection · chain D against D, TM-score 1.00
P49711 · AlphaFold monomer V2.0 prediction for transcriptional repressor ctcf (P49711) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 5YEH · PDBe 5YEH · UniProt P49711

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