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2qkk

Human RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid

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

Ribonuclease H1

Homo sapiens

UniProt O60930

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Homooligomer Protein 2 DNA 1 RNA 1 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' × 1 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3' × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CALCIUM ION × 3 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 1 water × 4 Consistent with all polymers
2 Other combination Homooligomer Protein 2 DNA 1 RNA 1 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' × 1 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3' × 1 CALCIUM ION × 3 water × 4 Consistent with all polymers
3 Other combination Homooligomer Protein 2 DNA 1 RNA 1 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' × 1 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3' × 1 CALCIUM ION × 2 water × 4 Consistent with all polymers
4 Other combination Homooligomer Protein 2 DNA 1 RNA 1 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' × 1 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3' × 1 CALCIUM ION × 3 water × 4 Consistent with all polymers
5 Other combination Homooligomer Protein 2 DNA 1 RNA 1 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' × 1 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3' × 1 CALCIUM ION × 2 water × 4 Consistent with all polymers
6 Other combination Monomer Protein 1 DNA 1 RNA 1 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' × 1 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3' × 1 CALCIUM ION × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qk9 2qkb 2qkk 2qkk 2qkk 2qkk 2qkk 2qkk 3bsu 3bsu 6vrd 8swb

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RNH1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 4–154； UniProt 136–286 Author chain B； PDBConstruct 4–154； UniProt 136–286 Author chain E； PDBConstruct 4–154； UniProt 136–286 Author chain F； PDBConstruct 4–154； UniProt 136–286 Author chain I； PDBConstruct 4–154； UniProt 136–286 Author chain J； PDBConstruct 4–154； UniProt 136–286 Author chain M； PDBConstruct 4–154； UniProt 136–286 Author chain N； PDBConstruct 4–154； UniProt 136–286 Author chain R； PDBConstruct 4–154； UniProt 136–286 Author chain S； PDBConstruct 4–154； UniProt 136–286 Author chain W； PDBConstruct 4–154； UniProt 136–286

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_id2qkk
Deposition date deposition_date2007-07-11
Structure title titleHuman RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid
Keywords keywordsRNase H; RNA/DNA hybrid, HYDROLASE-DNA-RNA COMPLEX; HYDROLASE/DNA/RNA
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.

2qkk__assembly_1__model_1

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

Download this curve (.dat)

2qkk__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.

2qkk__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）24.24 Å
Rg (electron density)24.79 Å
Total Rg25.33 Å
Atom count2964
Residues333
Excluded volume50223 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qkk__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2qkk__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2qkk__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2qkk__assembly_4__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 2qkk__assembly_5__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 2qkk__assembly_6__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 (8)

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id2qkkA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkM00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkN00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkR00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkS00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2qkkW00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
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7. Citations (1)