3lwl

Structure of Klenow fragment of Taq polymerase in complex with an abasic site

Method: X-RAY DIFFRACTION

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

DNA polymerase I, thermostable

Thermus aquaticus

UniProt P19821

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCP(2DA))-3') ; × 1 ;DNA (5'-D(APAPAP(3DR)PTPGPCPGPCPCPGPTPGPGPTPC)-3') ; × 1 ;2',3'-dideoxyadenosine triphosphate ; × 1 MAGNESIUM ION × 1 ACETATE ION × 5 GLYCEROL × 7 SODIUM ION × 4 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO1_THEAQ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–540； UniProt 293–832

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	3lwl
Deposition date deposition_date	2010-02-24
Structure title title	Structure of Klenow fragment of Taq polymerase in complex with an abasic site
Keywords keywords	;DNA replication, DNA repair, DNA polymerases, Abasic sites, Translesion synthesis, DNA damage, DNA-binding, DNA-directed DNA polymerase, amino acid-templating mechanism, TRANSFERASE-DNA complex ;; TRANSFERASE/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.

3lwl__assembly_1__model_1

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

Download this curve (.dat)

3lwl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lwl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.80 Å
Rg (electron density)	25.10 Å
Total Rg	25.76 Å
Atom count	4852
Residues	558
Excluded volume	84862 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lwl__assembly_1__model_1`	trimeric （3）	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 (9)

Entity 1 Entity 1 polymer

Description description	DNA polymerase I, thermostable
Molecular weight formula_weight	60937.0 kDa
EC 编号 ec_number	2.7.7.7
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	5013

ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE

Source Source

Source organism organism	Thermus aquaticus
NCBI taxonomy ID ncbi_taxonomy_id	271
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCP(2DA))-3') ;
Molecular weight formula_weight	3641.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

GACCACGGCGCA

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APAPAP(3DR)PTPGPCPGPCPCPGPTPGPGPTPC)-3') ;
Molecular weight formula_weight	4790.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AAANTGCGCCGTGGTC

Entity 4 Entity 4 non-polymer

Description description	;2',3'-dideoxyadenosine triphosphate ;
Molecular weight formula_weight	475.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3lwlA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	3lwlA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1060 — Taq DNA Polymerase; Chain T, domain 4
Homologous superfamily homologous superfamily	10 — Taq DNA Polymerase; Chain T, domain 4

Domain ID domain_id	3lwlA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	3lwlA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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Unit-cell length a length_a	110.228 Å
Unit-cell length b length_b	110.228 Å
Unit-cell length c length_c	91.265 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	47.730 Å
R factor r_factor	0.1906
R_work r_work	0.1883
R_free r_free	0.2335

Structure of Klenow fragment of Taq polymerase in complex with an abasic site

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

DNA polymerase I, thermostable

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

3lwl__assembly_1__model_1

3lwl__assembly_1__model_1 | I(q)

3lwl__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of Klenow fragment of Taq polymerase in complex with an abasic site

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

DNA polymerase I, thermostable

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

3lwl__assembly_1__model_1

3lwl__assembly_1__model_1 | I(q)

3lwl__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)