1yau

Structure of Archeabacterial 20S proteasome- PA26 complex

Method: X-RAY DIFFRACTION

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

Proteasome alpha subunit

Thermoplasma acidophilum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	Proteasome beta subunit × 14 （P28061） proteasome activator protein PA26 × 14 SULFATE ION × 50 GLYCEROL × 14 water × 42	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSMA_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–233； UniProt 1–233 Author chain B； PDBConstruct 1–233； UniProt 1–233 Author chain C； PDBConstruct 1–233； UniProt 1–233 Author chain D； PDBConstruct 1–233； UniProt 1–233 Author chain E； PDBConstruct 1–233； UniProt 1–233 Author chain F； PDBConstruct 1–233； UniProt 1–233 Author chain G； PDBConstruct 1–233； UniProt 1–233

Proteasome beta subunit

Thermoplasma acidophilum

UniProt P28061

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	Proteasome alpha subunit × 14 （P25156） proteasome activator protein PA26 × 14 SULFATE ION × 50 GLYCEROL × 14 water × 42	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSMB_THEAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–211； UniProt 1–211 Author chain I； PDBConstruct 1–211； UniProt 1–211 Author chain J； PDBConstruct 1–211； UniProt 1–211 Author chain K； PDBConstruct 1–211； UniProt 1–211 Author chain L； PDBConstruct 1–211； UniProt 1–211 Author chain M； PDBConstruct 1–211； UniProt 1–211 Author chain N； PDBConstruct 1–211； UniProt 1–211

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	1yau
Deposition date deposition_date	2004-12-17
Structure title title	Structure of Archeabacterial 20S proteasome- PA26 complex
Keywords keywords	proteasome 20S, PA26 proteasome activator 11S, HYDROLASE-HYDROLASE ACTIVATOR COMPLEX; HYDROLASE/HYDROLASE ACTIVATOR
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.

1yau__assembly_1__model_1

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

Download this curve (.dat)

1yau__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yau__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	80.34 Å
Rg (electron density)	81.07 Å
Total Rg	80.76 Å
Atom count	69830
Residues	9002
Excluded volume	1250800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yau__assembly_1__model_1`	42-meric （42）	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 (6)

Entity 1 Entity 1 polymer

Description description	Proteasome alpha subunit
Molecular weight formula_weight	25665.3 kDa
EC 编号 ec_number	3.4.25.1
Mutation mutation	Y8G, D9G
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	36610

MQQGQMAGGRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL

Source Source

Source organism organism	Thermoplasma acidophilum
NCBI taxonomy ID ncbi_taxonomy_id	2303
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Proteasome beta subunit
Molecular weight formula_weight	23998.7 kDa
EC 编号 ec_number	3.4.25.1
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J,K,L,M,N

MNQTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVGGIDTAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDGYVQLPTDQIESRIRKLGLILHHHHHH

Source Source

Source organism organism	Thermoplasma acidophilum
NCBI taxonomy ID ncbi_taxonomy_id	2303
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	proteasome activator protein PA26
Molecular weight formula_weight	26087.6 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,S,T,U

MHHHHHHPPKRAALIQNLRDSYTETSSFAVIEEWAAGTLQEIEGIAKAAAEAHGVIRNSTYGRAQAEKSPEQLLGVLQRYQDLCHNVYCQAETIRTVIAIRIPEHKEEDNLGVAVQHAVLKIIDELEIKTLGSGEKSGSGGAPTPIGMYALREYLSARSTVEDKLLGSVDAESGKTKGGSQSPSLLLELRQIDADFMLKVELATTHLSTMVRAVINAYLLNWKKLIQPRTGSDHMVS

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	25

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1571

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6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

Domain ID domain_id	d1yaua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yauc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaud_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaue_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yauf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaug_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yauh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaui_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yauj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yauk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaul_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaum_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yaun_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d1yauo_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

Domain ID domain_id	d1yaup_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

Domain ID domain_id	d1yauq_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

Domain ID domain_id	d1yaur_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

Domain ID domain_id	d1yaus_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

Domain ID domain_id	d1yaut_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

Domain ID domain_id	d1yauu_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.8 — Proteasome activator
Family Family family	a.24.8.1 — Proteasome activator

CATH v4.4 (21 domains)

Domain ID domain_id	1yauA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauC00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauE00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauF00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauG00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauH00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauI00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauJ00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauK00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauL00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauM00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauN00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1yauO01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

Domain ID domain_id	1yauP01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

Domain ID domain_id	1yauQ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

Domain ID domain_id	1yauR01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

Domain ID domain_id	1yauS01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

Domain ID domain_id	1yauT01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

Domain ID domain_id	1yauU01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	180 — Proteasome activator pa28, C-terminal domain

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Unit-cell length a length_a	255.224 Å
Unit-cell length b length_b	126.913 Å
Unit-cell length c length_c	181.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1804
R_work r_work	0.1801
R_free r_free	0.2329

Structure of Archeabacterial 20S proteasome- PA26 complex

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

Proteasome alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Proteasome beta subunit

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

1yau__assembly_1__model_1

1yau__assembly_1__model_1 | I(q)

1yau__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

CATH v4.4 (21 domains)

7. Citations (1)

Structure of Archeabacterial 20S proteasome- PA26 complex

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

Proteasome alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Proteasome beta subunit

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

1yau__assembly_1__model_1

1yau__assembly_1__model_1 | I(q)

1yau__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

CATH v4.4 (21 domains)

7. Citations (1)