SAXSdb — 5npv

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

Autophagy protein 5

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–275	Not recorded	Autophagy-related protein 16-1 × 1 （Q676U5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.76；293 K；0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350	Resolution 3.10 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–275	Not recorded	Autophagy-related protein 16-1 × 1 （Q676U5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.76；293 K；0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350	Resolution 3.10 Å R-free 0.278

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 5NPV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GDK Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31	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 B 1–275（275 aa） Chain E 1–275（275 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M Hepes pH7.5, 0.2 M lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.236
4GDL Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–275（275 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.88 Å R-free 0.254
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–275（275 aa）	Not recorded	SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–275（275 aa）	Not recorded	SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 1–275（275 aa）	Not recorded	SO4 SULFATE ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–275（275 aa）	Not recorded	SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ1 Crystal structure of human ATG5-TECAIR Deposited 2014-06-10	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；MPD, PEG 1000, PEG 3350, alcohols, MES-imdazole	Resolution 1.80 Å R-free 0.222
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–275（275 aa） Chain C 1–275（275 aa）	Mutation：E122D Mutation：E122D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT	Resolution 3.00 Å R-free 0.244
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–275（275 aa） Chain G 1–275（275 aa）	Mutation：E122D Mutation：E122D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT	Resolution 3.00 Å R-free 0.244
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
7W36 Crystal structure of human Atg5 complexed with a stapled peptide Deposited 2021-11-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–275（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl pH8.5	Resolution 3.00 Å R-free 0.287

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

View Construct and Data Evidence

UniProt name	ATG5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–282； UniProt 1–275 Author chain C； PDBConstruct 8–282； UniProt 1–275

Autophagy-related protein 16-1

Homo sapiens

UniProt Q676U5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 11–307	Not recorded	Autophagy protein 5 × 1 （Q9H1Y0）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.76；293 K；0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350	Resolution 3.10 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 11–307	Not recorded	Autophagy protein 5 × 1 （Q9H1Y0）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.76；293 K；0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350	Resolution 3.10 Å R-free 0.278

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 5NPV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GDK Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31	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 C 11–43（33 aa） Chain F 11–43（33 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M Hepes pH7.5, 0.2 M lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.236
4GDL Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 11–43（33 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.88 Å R-free 0.254
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain O 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–69（69 aa） Fragment：UNP residues 1-69 Chain D 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT	Resolution 3.00 Å R-free 0.244
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–69（69 aa） Fragment：UNP residues 1-69 Chain H 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT	Resolution 3.00 Å R-free 0.244
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NUV Structure of the WD40-domain of human ATG16L1 Deposited 2017-05-02	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 303–607（305 aa）	Mutation：E354A/K355A/Y607P	BU3 (R,R)-2,3-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；303 K；1.61 M (NH4)2SO4, 0.09 M NaCl, 0.1 M MES pH 6.3	Resolution 1.55 Å R-free 0.197
7W36 Crystal structure of human Atg5 complexed with a stapled peptide Deposited 2021-11-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 13–33（21 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl pH8.5	Resolution 3.00 Å R-free 0.287
7XFR Crystal structure of WIPI2b in complex with the second site of ATG16L1 Deposited 2022-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 124–188（65 aa） Chain D 124–188（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M MES monohydrate(pH 6.5), 12% w/v Polyethylene glycol 20000	Resolution 1.76 Å R-free 0.193
8ZQG Crystal structure of WIPI3 in complex with ATG16L1 Deposited 2024-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 124–188（65 aa） Chain D 124–188（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；289 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8); 16% w/v Polyethylene glycol 3350	Resolution 2.77 Å R-free 0.233
9H2Q Stabilized complex of Chlamydia trachomatic efector CT622 in complex with human WD40 domain of ATG16L1 Deposited 2024-10-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 303–607（305 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
9J54 Crystal structure of FIP200 Claw in complex with ATG16L1 Deposited 2024-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 235–247（13 aa） Chain D 235–247（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；10% v/v 2-Propanol, 0.1 M BICINE (pH 8.5), 30% w/v Polyethylene glycol 1500	Resolution 1.61 Å R-free 0.216
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 235–247（13 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000	Resolution 1.76 Å R-free 0.215
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 235–247（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000	Resolution 1.76 Å R-free 0.215

13 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A16L1_HUMAN
Isoform	Q676U5-3
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–301； UniProt 11–307 Author chain D； PDBConstruct 5–301； UniProt 11–307

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5npv
Deposition date deposition_date	2017-04-19
Structure title title	Structure of human ATG5-ATG16L1(ATG5BD) complex (I4)
Keywords keywords	autophagy, ATG16L1, ATG5, CELL CYCLE; CELL CYCLE
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	28.51 Å
Radius of gyration Rg (electron density) rg_electron	27.52 Å
Forward intensity I(0) i0	65048300.00
Molecular weight molecular_weight	65341.0 kDa
Excluded volume excluded_volume	82675 Å³
Envelope volume envelope_volume	102840 Å³
Hydration-shell volume shell_volume	31241 Å³
Envelope diameter envelope_diameter	94.2 Å
Shell Rg shell_rg	34.56 Å
Envelope Rg envelope_rg	27.60 Å
Shape Rg shape_rg	27.50 Å
Total Rg total_rg	28.36 Å
Total atoms total_atoms	9044
Residues n_residues	569
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	91.8 Å
Rg (real space) rg_real	28.51 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	6.5050e+07
I(0) uncertainty (real space) i0_real_error	9.1480e+05
Rg (reciprocal space) rg_reciprocal	28.51 Å
I(0) (reciprocal space) i0_reciprocal	65050000.0000
Solution quality estimate total_estimate	0.8992
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.312
Kurtosis Kurtosis kurtosis	-0.520
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19920000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.953

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Autophagy protein 5
Molecular weight formula_weight	33188.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9055

GAHMSGRMTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Autophagy-related protein 16-1
Molecular weight formula_weight	34789.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GGGRPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRKDREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKLRKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLLDSITNIFGRRSVSSFPVPQDNVDTHPGSGKE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5npvA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5npvA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	5npvA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	190 — Autophagy protein Apg5, helix rich domain

Domain ID domain_id	5npvC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5npvC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	5npvC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	190 — Autophagy protein Apg5, helix rich domain

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8. Citations (1)

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Unit-cell length a length_a	143.580 Å
Unit-cell length b length_b	143.580 Å
Unit-cell length c length_c	62.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	45.404 Å
R factor r_factor	0.2543
R_work r_work	0.2529
R_free r_free	0.2781

fit	/app/data/saxs_computation/np/5npv/5npv.fit
pddf	/app/data/pr_computation/np/5npv/5npv.pr.out
profile	/app/data/saxs_computation/np/5npv/5npv.dat

Structure of human ATG5-ATG16L1(ATG5BD) complex (I4)

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

Autophagy protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Autophagy-related protein 16-1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)