3u5z

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog

Method: X-RAY DIFFRACTION

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

DNA polymerase accessory protein 44

Enterobacteria phage T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	DNA polymerase accessory protein 62 × 1 （P04527） DNA polymerase processivity component × 3 （P04525） Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 8 DNA 2	DNA polymerase accessory protein 62 × 1 （P04527） DNA polymerase processivity component × 3 （P04525） Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPA44_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 6–324； UniProt 1–319 Author chain C； PDBConstruct 6–324； UniProt 1–319 Author chain D； PDBConstruct 6–324； UniProt 1–319 Author chain E； PDBConstruct 6–324； UniProt 1–319 Author chain L； PDBConstruct 6–324； UniProt 1–319 Author chain M； PDBConstruct 6–324； UniProt 1–319 Author chain N； PDBConstruct 6–324； UniProt 1–319 Author chain O； PDBConstruct 6–324； UniProt 1–319

DNA polymerase accessory protein 62

Enterobacteria phage T4

UniProt P04527

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	DNA polymerase accessory protein 44 × 4 （P04526） DNA polymerase processivity component × 3 （P04525） Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 8 DNA 2	DNA polymerase accessory protein 44 × 4 （P04526） DNA polymerase processivity component × 3 （P04525） Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPA62_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 2–187 Author chain K； PDBConstruct 1–186； UniProt 2–187

DNA polymerase processivity component

Enterobacteria phage T4

UniProt P04525

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	DNA polymerase accessory protein 44 × 4 （P04526） DNA polymerase accessory protein 62 × 1 （P04527） Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 8 DNA 2	DNA polymerase accessory protein 44 × 4 （P04526） DNA polymerase accessory protein 62 × 1 （P04527） Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPA5_BPT4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–228； UniProt 1–228 Author chain G； PDBConstruct 1–228； UniProt 1–228 Author chain H； PDBConstruct 1–228； UniProt 1–228 Author chain P； PDBConstruct 1–228； UniProt 1–228 Author chain Q； PDBConstruct 1–228； UniProt 1–228 Author chain R； PDBConstruct 1–228； UniProt 1–228

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	3u5z
Deposition date deposition_date	2011-10-11
Structure title title	Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog
Keywords keywords	AAA+, ATP hydrolase, clamp loader, sliding clamp, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

3u5z__assembly_1__model_1

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

Download this curve (.dat)

3u5z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u5z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.85 Å
Rg (electron density)	40.89 Å
Total Rg	41.29 Å
Atom count	17712
Residues	2161
Excluded volume	313920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u5z__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3u5z__assembly_2__model_1`	decameric （10）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA polymerase accessory protein 44
Molecular weight formula_weight	36189.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,E,L,M,N,O
Atom count atom_count	35424

GPGGSMITVNEKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDCKIDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYSSKGVLDAGILSLVTNDRGAIDDVLESLKNKDVKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSIIRMYEIVGENNQYHGIAANTELHLAYLFIQLACEMQWK

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase accessory protein 62
Molecular weight formula_weight	22941.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,K

SLFKDDIQLNEHQVAWYSKDWTAVQSAADSFKEKAENEFFEIIGAINNKTKCSIAQKDYSKFMVENALSQFPECMPAVYAMNLIGSGLSDEAHFNYLMAAVPRGKRYGKWAKLVEDSTEVLIIKLLAKRYQVNTNDAINYKSILTKNGKLPLVLKELKGLVTDDFLKEVTKNVKEQKQLKKLALEWGLEHHHHHHHHHH

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA polymerase processivity component
Molecular weight formula_weight	25162.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,F,Q,R,P

MKLSKDTTALLKNFATINSGIMLKSGQFIMTRAVNGTTYAEANISDVIDFDVAIYDLNGFLGILSLVNDDAEISQSEDGNIKIADARSTIFWPAADPSTVVAPNKPIPFPVASAVTEIKAEDLQQLLRVSRGLQIDTIAITVKEGKIVINGFNKVEDSALTRVKYSLTLGDYDGENTFNFIINMANMKMQPGNYKLLLWAKGKQGAAKFEGEHANYVVALEADSTHDF

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Template DNA strand
Molecular weight formula_weight	9172.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,S

TTTTTTTTTTTATGTACTCGTAGTGTCTGC

Entity 5 Entity 5 polymer

Description description	Primer DNA strand
Molecular weight formula_weight	6136.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,T

GCAGACACTACGAGTACATA

Entity 6 Entity 6 non-polymer

Description description	;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ;
Molecular weight formula_weight	492.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

Domain ID domain_id	3u5zA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1260 —

Domain ID domain_id	3u5zA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	50 — Bacteriophage clamp loader A subunit, A' domain

Domain ID domain_id	3u5zA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	700 — Bacteriophage clamp loader A subunit, A domain

Domain ID domain_id	3u5zB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zE03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zF00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zG00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zH00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zK01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1260 —

Domain ID domain_id	3u5zK02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	50 — Bacteriophage clamp loader A subunit, A' domain

Domain ID domain_id	3u5zK03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	700 — Bacteriophage clamp loader A subunit, A domain

Domain ID domain_id	3u5zL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zL02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zL03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zM02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zM03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zN01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zN02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zN03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zO01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3u5zO02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3u5zO03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zP00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zQ00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3u5zR00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	95.702 Å
Unit-cell length b length_b	239.177 Å
Unit-cell length c length_c	247.672 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	49.193 Å
R factor r_factor	0.2322
R_work r_work	0.2309
R_free r_free	0.2787

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog

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

DNA polymerase accessory protein 44

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase accessory protein 62

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase processivity component

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

3u5z__assembly_1__model_1

3u5z__assembly_1__model_1 | I(q)

3u5z__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 (8)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

7. Citations (1)