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1rzt

Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase lambda

Homo sapiens

UniProt Q9UGP5

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 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' × 1 5'-D(*GP*TP*GP*CP*G)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 SODIUM ION × 3 water × 4 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' × 1 5'-D(*GP*TP*GP*CP*G)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 SODIUM ION × 2 water × 4 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' × 1 5'-D(*GP*TP*GP*CP*G)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 SODIUM ION × 3 water × 4 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' × 1 5'-D(*GP*TP*GP*CP*G)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 SODIUM ION × 2 1,2-ETHANEDIOL × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1nzp 2jw5 4xq8 4xrh 5ca7 5cb1 5cb1 5chg 5cj7 5cp2 5cr0 5ddm

16 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1rzt 1rzt 1rzt 1rzt 1xsl 1xsl 1xsl 1xsl 1xsn 1xsp 2bcq 2bcr

127 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPOL_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 1–331； UniProt 245–575 Author chain E； PDBConstruct 1–331； UniProt 245–575 Author chain I； PDBConstruct 1–331； UniProt 245–575 Author chain M； PDBConstruct 1–331； UniProt 245–575

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_id1rzt
Deposition date deposition_date2003-12-29
Structure title titleCrystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule
Keywords keywordsDNA polymerase lambda, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
Experimental Method methodX-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.

1rzt__assembly_1__model_1

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

Download this curve (.dat)

1rzt__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1rzt__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）22.73 Å
Rg (electron density)22.06 Å
Total Rg22.81 Å
Atom count2966
Residues347
Excluded volume51224 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1rzt__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1rzt__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1rzt__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1rzt__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 (7)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1rzta1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family familya.60.6.1 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_idd1rzta2
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.12 — PsbU/PolX domain-like
Family Family familya.60.12.1 — DNA polymerase beta-like, second domain
Domain ID domain_idd1rzta3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.218 — Nucleotidyltransferase
Superfamily Superfamily superfamilyd.218.1 — Nucleotidyltransferase
Family Family familyd.218.1.2 — DNA polymerase beta-like
Domain ID domain_idd1rzte1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family familya.60.6.1 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_idd1rzte2
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.12 — PsbU/PolX domain-like
Family Family familya.60.12.1 — DNA polymerase beta-like, second domain
Domain ID domain_idd1rzte3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.218 — Nucleotidyltransferase
Superfamily Superfamily superfamilyd.218.1 — Nucleotidyltransferase
Family Family familyd.218.1.2 — DNA polymerase beta-like
Domain ID domain_idd1rzti1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family familya.60.6.1 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_idd1rzti2
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.12 — PsbU/PolX domain-like
Family Family familya.60.12.1 — DNA polymerase beta-like, second domain
Domain ID domain_idd1rzti3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.218 — Nucleotidyltransferase
Superfamily Superfamily superfamilyd.218.1 — Nucleotidyltransferase
Family Family familyd.218.1.2 — DNA polymerase beta-like
Domain ID domain_idd1rztm1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family familya.60.6.1 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_idd1rztm2
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.12 — PsbU/PolX domain-like
Family Family familya.60.12.1 — DNA polymerase beta-like, second domain
Domain ID domain_idd1rztm3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.218 — Nucleotidyltransferase
Superfamily Superfamily superfamilyd.218.1 — Nucleotidyltransferase
Family Family familyd.218.1.2 — DNA polymerase beta-like

CATH v4.4 (16 domains)

Domain ID domain_id1rztA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily110 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_id1rztA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1rztA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
Domain ID domain_id1rztA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily10 — DNA polymerase, thumb domain
Domain ID domain_id1rztE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily110 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_id1rztE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1rztE03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
Domain ID domain_id1rztE04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily10 — DNA polymerase, thumb domain
Domain ID domain_id1rztI01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily110 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_id1rztI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1rztI03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
Domain ID domain_id1rztI04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily10 — DNA polymerase, thumb domain
Domain ID domain_id1rztM01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily110 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_id1rztM02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1rztM03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
Domain ID domain_id1rztM04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily10 — DNA polymerase, thumb domain
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7. Citations (1)