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1zq1

Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi

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

Glutamyl-tRNA(Gln) amidotransferase subunit D

Pyrococcus abyssi

UniProt Q9V0T9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Glutamyl-tRNA(Gln) amidotransferase subunit E × 2 （Q9V0U0） ASPARTIC ACID × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1zq1

1 assemblies

View Construct and Data Evidence
UniProt name GATD_PYRAB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–438； UniProt 1–438 Author chain B； PDBConstruct 1–438； UniProt 1–438

Glutamyl-tRNA(Gln) amidotransferase subunit E

Pyrococcus abyssi

UniProt Q9V0U0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Glutamyl-tRNA(Gln) amidotransferase subunit D × 2 （Q9V0T9） ASPARTIC ACID × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1zq1

1 assemblies

View Construct and Data Evidence
UniProt name GATE_PYRAB
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–633； UniProt 1–633 Author chain D； PDBConstruct 1–633； UniProt 1–633

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_id1zq1
Deposition date deposition_date2005-05-18
Structure title titleStructure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi
Keywords keywordsx-ray; 3D structure; asparaginase 1 family; GatD subfamily, LYASE; LYASE
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.

1zq1__assembly_1__model_1

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

Download this curve (.dat)

1zq1__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1zq1__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）45.25 Å
Rg (electron density)45.60 Å
Total Rg45.39 Å
Atom count14801
Residues1862
Excluded volume265360 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1zq1__assembly_1__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 (4)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd1zq1a1
Class classb — All beta proteins
Fold Fold foldb.38 — Sm-like fold
Superfamily Superfamily superfamilyb.38.3 — GatD N-terminal domain-like
Family Family familyb.38.3.1 — GatD N-terminal domain-like
Domain ID domain_idd1zq1a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamilyc.88.1 — Glutaminase/Asparaginase
Family Family familyc.88.1.1 — Glutaminase/Asparaginase
Domain ID domain_idd1zq1b1
Class classb — All beta proteins
Fold Fold foldb.38 — Sm-like fold
Superfamily Superfamily superfamilyb.38.3 — GatD N-terminal domain-like
Family Family familyb.38.3.1 — GatD N-terminal domain-like
Domain ID domain_idd1zq1b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.88 — Glutaminase/Asparaginase
Superfamily Superfamily superfamilyc.88.1 — Glutaminase/Asparaginase
Family Family familyc.88.1.1 — Glutaminase/Asparaginase
Domain ID domain_idd1zq1c1
Class classa — All alpha proteins
Fold Fold folda.182 — GatB/YqeY motif
Superfamily Superfamily superfamilya.182.1 — GatB/YqeY motif
Family Family familya.182.1.2 — GatB/GatE C-terminal domain-like
Domain ID domain_idd1zq1c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.4 — GAD domain-like
Family Family familyd.74.4.1 — GAD domain
Domain ID domain_idd1zq1c3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamilyd.128.1 — Glutamine synthetase/guanido kinase
Family Family familyd.128.1.5 — GatB/GatE catalytic domain-like
Domain ID domain_idd1zq1d1
Class classa — All alpha proteins
Fold Fold folda.182 — GatB/YqeY motif
Superfamily Superfamily superfamilya.182.1 — GatB/YqeY motif
Family Family familya.182.1.2 — GatB/GatE C-terminal domain-like
Domain ID domain_idd1zq1d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.4 — GAD domain-like
Family Family familyd.74.4.1 — GAD domain
Domain ID domain_idd1zq1d3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamilyd.128.1 — Glutamine synthetase/guanido kinase
Family Family familyd.128.1.5 — GatB/GatE catalytic domain-like

CATH v4.4 (10 domains)

Domain ID domain_id1zq1A01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily520 —
Domain ID domain_id1zq1A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1170 — L-asparaginase, N-terminal domain
Domain ID domain_id1zq1A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1zq1B01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily520 —
Domain ID domain_id1zq1B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1170 — L-asparaginase, N-terminal domain
Domain ID domain_id1zq1B03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1zq1C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily30 — GAD-like domain
Domain ID domain_id1zq1C03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily380 — GatB domain, N-terminal subdomain
Domain ID domain_id1zq1D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily30 — GAD-like domain
Domain ID domain_id1zq1D03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily380 — GatB domain, N-terminal subdomain
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7. Citations (1)