5iio

Crystal structure of the DNA polymerase lambda binary complex

Method: X-RAY DIFFRACTION

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

DNA polymerase lambda

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(CPGPGPCP(8OG)PGPTPAPCPTPG)-3') ; × 1 ;DNA (5'-D(CPAPGPTPAPC)-3') ; × 1 ;DNA (5'-D(PGPCPCP*G)-3') ; × 1 SODIUM ION × 2 water × 4	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(CPGPGPCP(8OG)PGPTPAPCPTPG)-3') ; × 1 ;DNA (5'-D(CPAPGPTPAPC)-3') ; × 1 ;DNA (5'-D(PGPCPCP*G)-3') ; × 1 SODIUM ION × 1 water × 4	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(CPGPGPCP(8OG)PGPTPAPCPTPG)-3') ; × 1 ;DNA (5'-D(CPAPGPTPAPC)-3') ; × 1 ;DNA (5'-D(PGPCPCP*G)-3') ; × 1 SODIUM ION × 1 water × 4	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(CPGPGPCP(8OG)PGPTPAPCPTPG)-3') ; × 1 ;DNA (5'-D(CPAPGPTPAPC)-3') ; × 1 ;DNA (5'-D(PGPCPCP*G)-3') ; × 1 SODIUM ION × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOLL_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–334； UniProt 242–575 Author chain E； PDBConstruct 1–334； UniProt 242–575 Author chain I； PDBConstruct 1–334； UniProt 242–575 Author chain M； PDBConstruct 1–334； UniProt 242–575

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	5iio
Deposition date deposition_date	2016-03-01
Structure title title	Crystal structure of the DNA polymerase lambda binary complex
Keywords keywords	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.

5iio__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5iio__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5iio__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.60 Å
Rg (electron density)	22.03 Å
Total Rg	22.75 Å
Atom count	2926
Residues	345
Excluded volume	50398 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5iio__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5iio__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5iio__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5iio__assembly_4__model_1`	tetrameric （4）	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	;DNA (5'-D(CPGPGPCP(8OG)PGPTPAPCPTP*G)-3') ;
Molecular weight formula_weight	3406.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,F,J,N
Atom count atom_count	13086

CGGCGGTACTG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPAPGPTPAPC)-3') ;
Molecular weight formula_weight	1793.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G,K,O

CAGTAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPCPCPG)-3') ;
Molecular weight formula_weight	1191.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H,L,P

GCCG

Entity 4 Entity 4 polymer

Description description	DNA polymerase lambda
Molecular weight formula_weight	37348.6 kDa
EC 编号 ec_number	2.7.7.7,4.2.99.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M

AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1213

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	5iioA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	5iioA02
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

Domain ID domain_id	5iioA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5iioA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	5iioE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	5iioE02
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

Domain ID domain_id	5iioE03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5iioE04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	5iioI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	5iioI02
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

Domain ID domain_id	5iioI03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5iioI04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	5iioM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	5iioM02
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

Domain ID domain_id	5iioM03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5iioM04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

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Unit-cell length a length_a	191.423 Å
Unit-cell length b length_b	98.980 Å
Unit-cell length c length_c	105.034 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	45.086 Å
R factor r_factor	0.1923
R_work r_work	0.1913
R_free r_free	0.2351

Crystal structure of the DNA polymerase lambda binary complex

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

DNA polymerase lambda

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

5iio__assembly_2__model_1

5iio__assembly_2__model_1 | I(q)

5iio__assembly_2__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of the DNA polymerase lambda binary complex

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

DNA polymerase lambda

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

5iio__assembly_2__model_1

5iio__assembly_2__model_1 | I(q)

5iio__assembly_2__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)