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3hx0

ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA

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*AP*TP*AP*CP*TP*G)-3' × 1 5'-D(*CP*AP*GP*TP*AP*T)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3' × 1 5'-D(*CP*AP*GP*TP*AP*T)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 1 water × 2 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3' × 1 5'-D(*CP*AP*GP*TP*AP*T)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 2 water × 2 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3' × 1 5'-D(*CP*AP*GP*TP*AP*T)-3' × 1 5'-D(P*GP*CP*CP*G)-3' × 1 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 2 water × 1 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 DPOLL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–335； UniProt 242–575 Author chain F； PDBConstruct 2–335； UniProt 242–575 Author chain K； PDBConstruct 2–335； UniProt 242–575 Author chain P； PDBConstruct 2–335； 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_id3hx0
Deposition date deposition_date2009-06-19
Structure title titleternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA
Keywords keywords;scrunch, X-family, polymerase lambda, DNA damage, DNA repair, DNA replication, DNA synthesis, DNA-binding, DNA-directed DNA polymerase, Lyase, Manganese, Metal-binding, Nucleotidyltransferase, Nucleus, Phosphoprotein, Polymorphism, Transferase, 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.

3hx0__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hx0__assembly_4__model_1 | I(q)

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

3hx0__assembly_4__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）22.39 Å
Rg (electron density)21.77 Å
Total Rg22.47 Å
Atom count2947
Residues349
Excluded volume50617 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3hx0__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3hx0__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3hx0__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3hx0__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 (8)

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id3hx0A01
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_id3hx0A02
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_id3hx0A03
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_id3hx0A04
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_id3hx0F01
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_id3hx0F02
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_id3hx0F03
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_id3hx0F04
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_id3hx0K01
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_id3hx0K02
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_id3hx0K03
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_id3hx0K04
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_id3hx0P01
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_id3hx0P02
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_id3hx0P03
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_id3hx0P04
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)