5m5s

Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif

Method: X-RAY DIFFRACTION D_max: 107.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Clathrin heavy chain 1

Bos taurus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–363	Not recorded	Amphiphysin × 2 （P49418） GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5	Resolution 1.88 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–363	Not recorded	Amphiphysin × 2 （P49418） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5	Resolution 1.88 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5M5S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B89 CLATHRIN HEAVY CHAIN PROXIMAL LEG SEGMENT (BOVINE) Deposited 1999-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1074–1522（449 aa） Fragment：PROXIMAL LEG	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；250 MM SODIUM FORMATE, 100 MM TRIS-HCL, PH 8, pH 8.0	Resolution 2.60 Å R-free 0.279
1UTC Clathrin terminal domain complexed with TLPWDLWTT Deposited 2003-12-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–363（363 aa） Fragment：TERMINAL DOMAIN, RESIDUES 1-363	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP	Resolution 2.30 Å R-free 0.253
1UTC Clathrin terminal domain complexed with TLPWDLWTT Deposited 2003-12-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–363（363 aa） Fragment：TERMINAL DOMAIN, RESIDUES 1-363	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP	Resolution 2.30 Å R-free 0.253
1XI4 Clathrin D6 Coat Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-MERIC	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25mM MES；pH 6.5；25mM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
1XI4 Clathrin D6 Coat Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25mM MES；pH 6.5；25mM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
1XI4 Clathrin D6 Coat Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25mM MES；pH 6.5；25mM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-MERIC	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
3GC3 Crystal Structure of Arrestin2S and Clathrin Deposited 2009-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–363（363 aa） Fragment：WD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM bis_tris propane 4 -4.5 M ammonium acetate 4.5% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.251
3GD1 Structure of an Arrestin/Clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking Deposited 2009-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 1–363（363 aa） Fragment：WD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；293 K；100mM Bicine, 7% O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500, 6% polyethylene glycol 8000, 4% acetone, 1% ethylene glycol and 10 mM strontium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.254
3IYV Clathrin D6 coat as full-length Triskelions Deposited 2010-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-meric	Chain A 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain B 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain C 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain D 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain E 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain F 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain G 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain H 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain I 1–1630（1630 aa） Fragment：UNP residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25MM MES；pH 6.5；25MM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
3IYV Clathrin D6 coat as full-length Triskelions Deposited 2010-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain B 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain C 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain D 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain E 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain F 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain G 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain H 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain I 1–1630（1630 aa） Fragment：UNP residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25MM MES；pH 6.5；25MM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
3IYV Clathrin D6 coat as full-length Triskelions Deposited 2010-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain B 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain C 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain D 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain E 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain F 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain G 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain H 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain I 1–1630（1630 aa） Fragment：UNP residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25MM MES；pH 6.5；25MM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
3LVG Crystal structure of a clathrin heavy chain and clathrin light chain complex Deposited 2010-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1074–1675（602 aa） Chain B 1074–1675（602 aa） Chain C 1074–1675（602 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200mM citrate, 16-22% glycerol, 2% trifluoroethanol, vapor diffusion, hanging drop, temperature 298K	Resolution 7.94 Å R-free 0.425
3LVH Crystal structure of a clathrin heavy chain and clathrin light chain complex Deposited 2010-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1074–1675（602 aa） Fragment：Hub Chain B 1074–1675（602 aa） Fragment：Hub Chain C 1074–1675（602 aa） Fragment：Hub	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200mM citrate, 16-22% glycerol, 2% trifluoroethanol, vapor diffusion, hanging drop, temperature 298K	Resolution 9.00 Å R-free 0.487
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain B 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain C 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain E 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain F 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain H 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain I 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain J 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain K 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain L 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain M 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain N 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain O 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain P 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain Q 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain R 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain S 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain T 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain U 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain V 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain W 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain X 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
5M5R Clathrin heavy chain N-terminal domain bound to beta2 adaptin clathrin box motif Deposited 2016-10-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；293 K；1 uL protein plus peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.94 M sodium malonate pH 6.7	Resolution 1.76 Å R-free 0.205
5M5T Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) Deposited 2016-10-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0	Resolution 1.70 Å R-free 0.185
5M5T Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) Deposited 2016-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0	Resolution 1.70 Å R-free 0.185
5M5U Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1) Deposited 2016-10-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0	Resolution 2.15 Å R-free 0.207
5M5U Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1) Deposited 2016-10-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0	Resolution 2.15 Å R-free 0.207
5M5V Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2) Deposited 2016-10-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0	Resolution 1.96 Å R-free 0.193
5M5V Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2) Deposited 2016-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0	Resolution 1.96 Å R-free 0.193
5M61 Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif Deposited 2016-10-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1	Resolution 1.84 Å R-free 0.182
5M61 Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif Deposited 2016-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1	Resolution 1.84 Å R-free 0.182
6WCJ Asymmetric vertex of the clathrin minicoat cage Deposited 2020-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–1675（1675 aa） Chain C 1–1675（1675 aa） Chain D 1–1675（1675 aa） Chain G 1–1675（1675 aa） Chain H 1–1675（1675 aa） Chain I 1–1675（1675 aa） Chain K 1–1675（1675 aa） Chain L 1–1675（1675 aa） Chain M 1–1675（1675 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
9F8T Clathrin terminal domain complexed with C-terminus of AAK1L Deposited 2024-05-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；20% PEG 3,350; 100 mM Bis-Tris propane, pH 6.0; 200 mM sodium citrate; 10 mM DTT	Resolution 1.71 Å R-free 0.209

17 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLH1_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–365； UniProt 1–363 Author chain B； PDBConstruct 3–365； UniProt 1–363

Amphiphysin

OrganismNot specified

UniProt P49418

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 349–358 Chain G； UniProt 349–358	Fragment：Clathrin-box motif, UNP residues 349-358	Clathrin heavy chain 1 × 1 （P49951） GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5	Resolution 1.88 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 349–358 Chain H； UniProt 349–358	Fragment：Clathrin-box motif, UNP residues 349-358	Clathrin heavy chain 1 × 1 （P49951） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5	Resolution 1.88 Å R-free 0.234

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5M5S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KY7 THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH AMPHIPHYSIN FXDXF Deposited 2002-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 322–330（9 aa） Fragment：RESIDUES 322-330	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.252
1UTC Clathrin terminal domain complexed with TLPWDLWTT Deposited 2003-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 379–387（9 aa） Fragment：W-BOX, RESIDUES 379-387	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP	Resolution 2.30 Å R-free 0.253
1UTC Clathrin terminal domain complexed with TLPWDLWTT Deposited 2003-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 379–387（9 aa） Fragment：W-BOX, RESIDUES 379-387	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP	Resolution 2.30 Å R-free 0.253
3SOG Crystal structure of the BAR domain of human Amphiphysin, isoform 1 Deposited 2011-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–236（203 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；277.15 K；2.66% PEG 6000, 2.66% PEG 8000, 2.66% PEG 10,000, 0.02M Magnesium Acetate, 0.05M Potassium Chloride, 0.1M MES, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.30 Å R-free 0.266
4ATM Crystal structure of the BAR domain of human Amphiphysin, isoform 1 at 1.8 Angstrom resolution featuring increased order at the N- terminus. Deposited 2012-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–242（242 aa） Fragment：RESIDUES 1-242	Not recorded	EDO 1,2-ETHANEDIOL × 10 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20% PEG 3350, 0.1 M CITRATE PH 5.5	Resolution 1.78 Å R-free 0.218
5M61 Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif Deposited 2016-10-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 349–360（12 aa） Fragment：extended Clathrin-box motif, UNP residues 349-360 Chain G 349–360（12 aa） Fragment：extended Clathrin-box motif, UNP residues 349-360	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1	Resolution 1.84 Å R-free 0.182
5M61 Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif Deposited 2016-10-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 349–360（12 aa） Fragment：extended Clathrin-box motif, UNP residues 349-360 Chain H 349–360（12 aa） Fragment：extended Clathrin-box motif, UNP residues 349-360	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1	Resolution 1.84 Å R-free 0.182

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPH_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–10； UniProt 349–358 Author chain F； PDBConstruct 1–10； UniProt 349–358 Author chain G； PDBConstruct 1–10； UniProt 349–358 Author chain H； PDBConstruct 1–10； UniProt 349–358

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5m5s
Deposition date deposition_date	2016-10-22
Structure title title	Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif
Keywords keywords	endocytosis; ENDOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.98 Å
Radius of gyration Rg (electron density) rg_electron	31.41 Å
Forward intensity I(0) i0	110016000.00
Molecular weight molecular_weight	84109.0 kDa
Excluded volume excluded_volume	105740 Å³
Envelope volume envelope_volume	134840 Å³
Hydration-shell volume shell_volume	36919 Å³
Envelope diameter envelope_diameter	113.6 Å
Shell Rg shell_rg	37.20 Å
Envelope Rg envelope_rg	31.41 Å
Shape Rg shape_rg	31.39 Å
Total Rg total_rg	32.00 Å
Total atoms total_atoms	5908
Residues n_residues	754
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.2 Å
Rg (real space) rg_real	32.13 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	1.1000e+08
I(0) uncertainty (real space) i0_real_error	1.6480e+06
Rg (reciprocal space) rg_reciprocal	32.07 Å
I(0) (reciprocal space) i0_reciprocal	110000000.0000
Solution quality estimate total_estimate	0.8678
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.460
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27060000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Clathrin heavy chain 1
Molecular weight formula_weight	40540.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6933

GSMAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEEL

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Amphiphysin
Molecular weight formula_weight	1177.3 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

ETLLDLDFDP

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	803

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5m5sA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	110 — Clathrin heavy-chain terminal domain

Domain ID domain_id	5m5sB00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	110 — Clathrin heavy-chain terminal domain

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8. Citations (1)

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Unit-cell length a length_a	139.967 Å
Unit-cell length b length_b	134.110 Å
Unit-cell length c length_c	78.012 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	67.060 Å
R factor r_factor	0.2056
R_work r_work	0.2042
R_free r_free	0.2339

fit	/app/data/saxs_computation/m5/5m5s/5m5s.fit
pddf	/app/data/pr_computation/m5/5m5s/5m5s.pr.out
profile	/app/data/saxs_computation/m5/5m5s/5m5s.dat

Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif

1. Protein Identity and Related Structures Protein Identity & Related Structures

Clathrin heavy chain 1

State in the Current Structure

Other States of the Same Protein in the Database

Amphiphysin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)