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3syt

Crystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi, NAD+, and glutamate

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

Glutamine-dependent NAD(+) synthetase

Mycobacterium tuberculosis

UniProt P0A5L6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 8 GLUTAMIC ACID × 8 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 8 ADENOSINE MONOPHOSPHATE × 8 PYROPHOSPHATE 2- × 8 GLYCEROL × 4 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
3dla 3sdb 3seq 3sez 3syt 3szg

6 assemblies

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name NADE_MYCTU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–680； UniProt 1–679 Author chain B； PDBConstruct 2–680； UniProt 1–679 Author chain C； PDBConstruct 2–680； UniProt 1–679 Author chain D； PDBConstruct 2–680； UniProt 1–679

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_id3syt
Deposition date deposition_date2011-07-18
Structure title titleCrystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi, NAD+, and glutamate
Keywords keywords;Glutamine-amidotransferase, Glutaminase, Glutamine-dependent NAD+ synthetase, Ligase, Ammonia tunneling, ATP binding, NAD, Nucleotide binding ;; LIGASE
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.

3syt__assembly_1__model_1

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

Download this curve (.dat)

3syt__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3syt__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）54.95 Å
Rg (electron density)54.63 Å
Total Rg54.78 Å
Atom count41098
Residues5240
Excluded volume724610 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3syt__assembly_1__model_1 octameric （8） 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) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3sytA01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily10 — Carbon-nitrogen hydrolase
Domain ID domain_id3sytA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3sytA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain
Domain ID domain_id3sytB01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily10 — Carbon-nitrogen hydrolase
Domain ID domain_id3sytB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3sytB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain
Domain ID domain_id3sytC01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily10 — Carbon-nitrogen hydrolase
Domain ID domain_id3sytC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3sytC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain
Domain ID domain_id3sytD01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily10 — Carbon-nitrogen hydrolase
Domain ID domain_id3sytD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id3sytD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain
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7. Citations (1)