1prt

THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN

Method: X-RAY DIFFRACTION

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

PERTUSSIS TOXIN (SUBUNIT S1)

Bordetella pertussis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOX1_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 36–269 Author chain G； PDBConstruct 1–234； UniProt 36–269

PERTUSSIS TOXIN (SUBUNIT S2)

Bordetella pertussis

UniProt P04978

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOX2_BORPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–196； UniProt 31–226 Author chain H； PDBConstruct 1–196； UniProt 31–226

PERTUSSIS TOXIN (SUBUNIT S3)

Bordetella pertussis

UniProt P04979

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOX3_BORPE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–196； UniProt 32–227 Author chain I； PDBConstruct 1–196； UniProt 32–227

PERTUSSIS TOXIN (SUBUNIT S4)

Bordetella pertussis

UniProt P0A3R5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S5) × 1 （P04981）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOX4_BORPE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–110； UniProt 43–152 Author chain E； PDBConstruct 1–110； UniProt 43–152 Author chain J； PDBConstruct 1–110； UniProt 43–152 Author chain K； PDBConstruct 1–110； UniProt 43–152

PERTUSSIS TOXIN (SUBUNIT S5)

Bordetella pertussis

UniProt P04981

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	PERTUSSIS TOXIN (SUBUNIT S1) × 1 （P04977） PERTUSSIS TOXIN (SUBUNIT S2) × 1 （P04978） PERTUSSIS TOXIN (SUBUNIT S3) × 1 （P04979） PERTUSSIS TOXIN (SUBUNIT S4) × 2 （P0A3R5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOX5_BORPE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–98； UniProt 36–133 Author chain L； PDBConstruct 1–98； UniProt 36–133

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	1prt
Deposition date deposition_date	1993-11-22
Structure title title	THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN
Keywords keywords	TOXIN; TOXIN
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.

1prt__assembly_1__model_1

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

Download this curve (.dat)

1prt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1prt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.59 Å
Rg (electron density)	29.81 Å
Total Rg	30.20 Å
Atom count	7252
Residues	934
Excluded volume	128930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1prt__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1prt__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 (5)

Entity 1 Entity 1 polymer

Description description	PERTUSSIS TOXIN (SUBUNIT S1)
Molecular weight formula_weight	26133.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G
Atom count atom_count	14504

DPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQAESSEAMAAWSERAGEAMVLVYYESIAYSF

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520

Entity 2 Entity 2 polymer

Description description	PERTUSSIS TOXIN (SUBUNIT S2)
Molecular weight formula_weight	21658.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520

Entity 3 Entity 3 polymer

Description description	PERTUSSIS TOXIN (SUBUNIT S3)
Molecular weight formula_weight	21622.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I

GIVIPPKALFTQQGGAYGRCPNGTRALTVAELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRLLYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520

Entity 4 Entity 4 polymer

Description description	PERTUSSIS TOXIN (SUBUNIT S4)
Molecular weight formula_weight	12072.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,J,K

DVPYVLVKTNMVVTSVAMKPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520

Entity 5 Entity 5 polymer

Description description	PERTUSSIS TOXIN (SUBUNIT S5)
Molecular weight formula_weight	10894.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,L

LPTHLYKNFTVQELALKLKGKNQEFCLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDLLELQICPLNGYCE

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1prta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1prtb1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prtb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.2 — Aerolysin/Pertussis toxin (APT) domain

Domain ID domain_id	d1prtc1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prtc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.2 — Aerolysin/Pertussis toxin (APT) domain

Domain ID domain_id	d1prtd_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prte_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prtf_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prtg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1prth1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prth2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.2 — Aerolysin/Pertussis toxin (APT) domain

Domain ID domain_id	d1prti1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prti2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.2 — Aerolysin/Pertussis toxin (APT) domain

Domain ID domain_id	d1prtj_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prtk_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d1prtl_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

CATH v4.4 (16 domains)

Domain ID domain_id	1prtA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	1prtB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	1prtB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	1prtC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtG00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	210 — Heat-Labile Enterotoxin; Chain A
Homologous superfamily homologous superfamily	10 — Heat-Labile Enterotoxin, subunit A

Domain ID domain_id	1prtH01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	1prtH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtI01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	40 — Pertussis Toxin; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Aerolysin/Pertussis toxin (APT), N-terminal domain

Domain ID domain_id	1prtI02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtJ00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtK00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1prtL00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

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Unit-cell length a length_a	163.800 Å
Unit-cell length b length_b	98.200 Å
Unit-cell length c length_c	194.500 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	—

THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN

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

PERTUSSIS TOXIN (SUBUNIT S1)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PERTUSSIS TOXIN (SUBUNIT S2)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PERTUSSIS TOXIN (SUBUNIT S3)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PERTUSSIS TOXIN (SUBUNIT S4)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PERTUSSIS TOXIN (SUBUNIT S5)

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

1prt__assembly_1__model_1

1prt__assembly_1__model_1 | I(q)

1prt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)