SAXSdb — 3w1s

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

Autophagy protein 5

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Autophagy protein 16 × 1 （Q03818） Ubiquitin-like protein ATG12 × 1 （P38316） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Autophagy protein 16 × 2 （Q03818） Ubiquitin-like protein ATG12 × 2 （P38316） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 1–284

Autophagy protein 16

Saccharomyces cerevisiae S288c

UniProt Q03818

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Autophagy protein 5 × 1 （Q12380） Ubiquitin-like protein ATG12 × 1 （P38316） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Autophagy protein 5 × 2 （Q12380） Ubiquitin-like protein ATG12 × 2 （P38316） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG16_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–49； UniProt 1–46

Ubiquitin-like protein ATG12

Saccharomyces cerevisiae S288c

UniProt P38316

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Autophagy protein 5 × 1 （Q12380） Autophagy protein 16 × 1 （Q03818） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Autophagy protein 5 × 2 （Q12380） Autophagy protein 16 × 2 （Q03818） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG12_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–91； UniProt 100–186

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	3w1s
Deposition date deposition_date	2012-11-20
Structure title title	Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16
Keywords keywords	Ubiquitin fold, E3-like, Atg3 binding, Isopeptide bond between Atg12 Gly186 and Atg5 Lys149, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3w1s__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3w1s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3w1s__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.14 Å
Rg (electron density)	20.88 Å
Total Rg	21.95 Å
Atom count	2868
Residues	362
Excluded volume	51641 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3w1s__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3w1s__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Autophagy protein 5
Molecular weight formula_weight	32620.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2895

MNDIKQLLWNGELNVLVSIDPSFLMKGSPREIAVLRIRVPRETYLVNYMPLIWNKIKSFLSFDPLTDSEKYFWFEHNKTPIPWNYPVGVLFDCLAGKSATFTTSFENQVKDVLTFLRIHLVMGDSLPPTIIPIASSKTQAEKFWFHQWKQVCFILNGSSKAIMSLSVNEARKFWGSVITRNFQDFIEISNKISSSRPRHIPLIIQTSRTSGTFRISQPTISMTGVNPTLKDIEGDILDVKEGINGNDVMVICQGIEIPWHMLLYDLYSKLRSFDGFLYITLVPI

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Autophagy protein 16
Molecular weight formula_weight	5792.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPHMGNFIITERKKAKEERSNPQTDSMDDLLIRRLTDRNDKEAHLNELF

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin-like protein ATG12
Molecular weight formula_weight	10341.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GAHMNIQKIQIKFQPIGSIGQLKPSVCKISMSQSFAMVILFLKRRLKMDHVYCYINNSFAPSPQQNIGELWMQFKTNDELIVSYCASVAFG

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3w1sc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3w1sA01
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	3w1sA02
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	3w1sA03
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	3w1sC00
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

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Unit-cell length a length_a	72.149 Å
Unit-cell length b length_b	106.084 Å
Unit-cell length c length_c	143.071 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	42.600 Å
R factor r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2580

Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16

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 protein 16

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein ATG12

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3w1s__assembly_1__model_1

3w1s__assembly_1__model_1 | I(q)

3w1s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Autophagy protein 16

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein ATG12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3w1s__assembly_1__model_1

3w1s__assembly_1__model_1 | I(q)

3w1s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)