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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P49711 New Search
21PDB entries
35Biological assembly
37chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1X6H Solution structures of the C2H2 type zinc finger domain of human Transcriptional repressor CTCF Deposited 2005-05-17 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 515–587（73 aa） Fragment：C2H2 type zinc finger domain
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.5mM C2H2 type zinc finger domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10uM ZnCl2; 10% D2O | 90% H2O/10% D2O
Resolution not provided
2CT1 Solution Structure of the zinc finger domain of Transcriptional repressor CTCF protein Deposited 2005-05-23 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 399–462（64 aa） Fragment：zinc finger domain
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient
NMR sample composition 2.46mM zinc finger domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
5K5H Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure Deposited 2016-05-23 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 348–464（117 aa） Fragment：unp residues 348-464
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% (w/v) polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris HCl, pH 5.5
Resolution 3.11 Å R-free 0.264
5K5I Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P65 Deposited 2016-05-23 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 378–489（112 aa） Fragment：unp residues 378-489
Not recorded ZN ZINC ION × 5 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；20% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5
Resolution 2.19 Å R-free 0.245
5K5J Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P41212 Deposited 2016-05-23 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 378–489（112 aa） Fragment：unp residues 378-489
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, and 0.1 M bis-tris HCl, pH 5.5
Resolution 2.29 Å R-free 0.254
5K5L Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure Deposited 2016-05-23 Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: heptameric（7） Consistent with all polymers
Chain E 405–492（88 aa） Fragment：unp residues 405-492
Chain F 405–492（88 aa） Fragment：unp residues 405-492
Chain G 405–492（88 aa） Fragment：unp residues 405-492
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；289 K；20% (w/v) polyethylene glycol 8,000 0.1 M CHES-NaOH pH 9.5
Resolution 3.12 Å R-free 0.270
5KKQ Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Deposited 2016-06-22 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 321–465（145 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5
Resolution 1.74 Å R-free 0.199
5KKQ Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Deposited 2016-06-22 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 321–465（145 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5
Resolution 1.74 Å R-free 0.199
5T00 Human CTCF ZnF3-7 and methylated DNA complex Deposited 2016-08-15 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 321–465（145 aa） Fragment：UNP residues 321-465
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5
Resolution 2.19 Å R-free 0.243
5T00 Human CTCF ZnF3-7 and methylated DNA complex Deposited 2016-08-15 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 321–465（145 aa） Fragment：UNP residues 321-465
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5
Resolution 2.19 Å R-free 0.243
5T0U CTCF ZnF2-7 and DNA complex structure Deposited 2016-08-16 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 294–465（172 aa） Fragment：UNP residues 294-465
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6
Resolution 3.20 Å R-free 0.266
5T0U CTCF ZnF2-7 and DNA complex structure Deposited 2016-08-16 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 294–465（172 aa） Fragment：UNP residues 294-465
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6
Resolution 3.20 Å R-free 0.266
5UND Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA Deposited 2017-01-30 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 348–547（200 aa）
Not recorded ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；28% PEG 2000 MME 100mM Bis-Tris, pH 6.5
Resolution 2.55 Å R-free 0.237
5UND Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA Deposited 2017-01-30 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain B 348–547（200 aa）
Not recorded ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；28% PEG 2000 MME 100mM Bis-Tris, pH 6.5
Resolution 2.55 Å R-free 0.237
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 292–490（199 aa） Fragment：UNP residues 292-490
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350
Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain B 292–490（199 aa） Fragment：UNP residues 292-490
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350
Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17 Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain G 292–490（199 aa） Fragment：UNP residues 292-490
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350
Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17 Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain J 292–490（199 aa） Fragment：UNP residues 292-490
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350
Resolution 2.81 Å R-free 0.254
5YEG Crystal structure of CTCF ZFs4-8-Hs5-1a complex Deposited 2017-09-17 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 349–490（142 aa） Fragment：UNP residues 349-490
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289.15 K；0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350
Resolution 2.00 Å R-free 0.204
5YEG Crystal structure of CTCF ZFs4-8-Hs5-1a complex Deposited 2017-09-17 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain B 349–489（141 aa） Fragment：UNP residues 349-489
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289.15 K；0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350
Resolution 2.00 Å R-free 0.204
5YEH Crystal structure of CTCF ZFs4-8-eCBS Deposited 2017-09-17 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 349–490（142 aa） Fragment：UNP residues 349-490
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350
Resolution 2.33 Å R-free 0.270
5YEH Crystal structure of CTCF ZFs4-8-eCBS Deposited 2017-09-17 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain B 349–490（142 aa） Fragment：UNP residues 349-490
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350
Resolution 2.33 Å R-free 0.270
5YEL Crystal structure of CTCF ZFs6-11-gb7CSE Deposited 2017-09-18 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain B 405–580（176 aa） Fragment：UNP residues 405-580
Mutation：C504S ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350
Resolution 2.96 Å R-free 0.286
5YEL Crystal structure of CTCF ZFs6-11-gb7CSE Deposited 2017-09-18 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 405–580（176 aa） Fragment：UNP residues 405-580
Mutation：C504S ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350
Resolution 2.96 Å R-free 0.286
6QNX Structure of the SA2/SCC1/CTCF complex Deposited 2019-02-12 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 222–231（10 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 2.70 Å
7W1M Cryo-EM structure of human cohesin-CTCF-DNA complex Deposited 2021-11-19 Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers
Chain H 1–727（727 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8SSQ ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 Deposited 2023-05-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 319–606（288 aa） Fragment：Zinc finger domains 3-11
Not recorded ZN ZINC ION × 9 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350
Resolution 3.12 Å R-free 0.271
8SSQ ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 Deposited 2023-05-08 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 319–606（288 aa） Fragment：Zinc finger domains 3-11
Not recorded ZN ZINC ION × 8 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350
Resolution 3.12 Å R-free 0.271
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 Deposited 2023-05-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 319–606（288 aa） Fragment：Zinc finger domains 3-11
Not recorded ZN ZINC ION × 9 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl
Resolution 3.14 Å R-free 0.284
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 Deposited 2023-05-08 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 319–606（288 aa） Fragment：Zinc finger domains 3-11
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl
Resolution 3.14 Å R-free 0.284
8SSS ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer Deposited 2023-05-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 263–465（203 aa） Fragment：Zinc finger domains 1-7
Not recorded ZN ZINC ION × 7 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；26.5% PEG3350, 0.26M DL-Malic acid 7.0
Resolution 2.30 Å R-free 0.231
8SSS ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer Deposited 2023-05-08 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 263–465（203 aa） Fragment：Zinc finger domains 1-7
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；26.5% PEG3350, 0.26M DL-Malic acid 7.0
Resolution 2.30 Å R-free 0.231
8SST ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer Deposited 2023-05-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 263–465（203 aa） Fragment：Zinc finger domains 1-7
Mutation：K365T ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.19 Å R-free 0.243
8SST ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer Deposited 2023-05-08 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain D 263–465（203 aa） Fragment：Zinc finger domains 1-7
Mutation：K365T ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.19 Å R-free 0.243
8SSU ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA Deposited 2023-05-08 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 320–582（263 aa） Fragment：Zinc finger domains 3-11 of CTCF, Residues 195-258 of LDB1
Not recorded EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane/pH 6.4, 20% w/v Polyethylene glycol 3,350
Resolution 2.89 Å R-free 0.240

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.