3dla

X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamine-dependent NAD(+) synthetase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	NICOTINIC ACID ADENINE DINUCLEOTIDE × 8 5-OXO-L-NORLEUCINE × 8 GLYCEROL × 30 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

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_id	3dla
Deposition date deposition_date	2008-06-26
Structure title title	X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON
Keywords keywords	;glutaminase, NAD+ synthetase, ammonia tunneling, enzyme, glutamine-dependent NAD+ synthetase, Glutamine-amido transferase, ATP-binding, Ligase, NAD, Nucleotide-binding ;; LIGASE
Experimental Method method	X-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.

3dla__assembly_1__model_1

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

Download this curve (.dat)

3dla__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dla__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	54.72 Å
Rg (electron density)	54.56 Å
Total Rg	54.70 Å
Atom count	41054
Residues	5228
Excluded volume	725580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dla__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 (5)

Entity 1 Entity 1 polymer

Description description	Glutamine-dependent NAD(+) synthetase
Molecular weight formula_weight	74855.4 kDa
EC 编号 ec_number	6.3.5.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	22006

SMNFYSAYQHGFVRVAACTHHTTIGDPAANAASVLDMARACHDDGAALAVFPELTLSGYSIEDVLLQDSLLDAVEDALLDLVTESADLLPVLVVGAPLRHRHRIYNTAVVIHRGAVLGVVPKSYLPTYREFYERRQMAPGDGERGTIRIGGADVAFGTDLLFAASDLPGFVLHVEICEDMFVPMPPSAEAALAGATVLANLSGSPITIGRAEDRRLLARSASARCLAAYVYAAAGEGESTTDLAWDGQTMIWENGALLAESERFPKGVRRSVADVDTELLRSERLRMGTFDDNRRHHRELTESFRRIDFALDPPAGDIGLLREVERFPFVPADPQRLQQDCYEAYNIQVSGLEQRLRALDYPKVVIGVSGGLDSTHALIVATHAMDREGRPRSDILAFALPGFATGEHTKNNAIKLARALGVTFSEIDIGDTARLMLHTIGHPYSVGEKVYDVTFENVQAGLRTDYLFRIANQRGGIVLGTGDLSELALGWSTYGVGDQMSHYNVNAGVPKTLIQHLIRWVISAGEFGEKVGEVLQSVLDTEITPELIPTGEEELQSSEAKVGPFALQDFSLFQVLRYGFRPSKIAFLAWHAWNDAERGNWPPGFPKSERPSYSLAEIRHWLQIFVQRFYSFSQFKRSALPNGPKVSHGGALSPRGDWRAPSDMSARIWLDQIDREVPKG

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINIC ACID ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	5-OXO-L-NORLEUCINE
Molecular weight formula_weight	145.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1443

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3dlaA01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	3dlaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	3dlaA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain

Domain ID domain_id	3dlaB01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	3dlaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	3dlaB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain

Domain ID domain_id	3dlaC01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	3dlaC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	3dlaC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain

Domain ID domain_id	3dlaD01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	110 — Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase
Homologous superfamily homologous superfamily	10 — Carbon-nitrogen hydrolase

Domain ID domain_id	3dlaD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	3dlaD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1140 — Glutamine-dependent NAD+ synthetase, C-terminal domain

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Unit-cell length a length_a	178.130 Å
Unit-cell length b length_b	178.130 Å
Unit-cell length c length_c	215.177 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	29.700 Å
R factor r_factor	0.1874
R_work r_work	0.1844
R_free r_free	0.2457

X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamine-dependent NAD(+) synthetase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dla__assembly_1__model_1

3dla__assembly_1__model_1 | I(q)

3dla__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamine-dependent NAD(+) synthetase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dla__assembly_1__model_1

3dla__assembly_1__model_1 | I(q)

3dla__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)