SAXSdb — 5ktn

▼

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

Quinolinate synthase A

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 1,3-DIHYDROXYACETONEPHOSPHATE × 1 CHLORIDE ION × 2 AMMONIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NADA_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–304； UniProt 1–300

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ktn
Deposition date deposition_date	2016-07-12
Structure title title	Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound dihydroxyacetone phosphate (DHAP) and Fe4S4 cluster
Keywords keywords	Dehydratase, iron-sulfur cluster, substrate complex, biosynthetic enzyme, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5ktn__assembly_1__model_1

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

Download this curve (.dat)

5ktn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ktn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.37 Å
Rg (electron density)	19.58 Å
Total Rg	20.29 Å
Atom count	2440
Residues	304
Excluded volume	44120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ktn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Quinolinate synthase A
Molecular weight formula_weight	34582.4 kDa
EC 编号 ec_number	2.5.1.72
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3243

GSFTMDLVEEILRLKEERNAIILAHNYQLPEVQDIADFIGDSLELARRATRVDADVIVFAGVDFMAETAKILNPDKVVLIPSREATCAMANMLKVEHILEAKRKYPNAPVVLYVNSTAEAKAYADVTVTSANAVEVVKKLDSDVVIFGPDKNLAHYVAKMTGKKIIPVPSKGHCYVHQKFTLDDVERAKKLHPNAKLMIHPECIPEVQEKADIIASTGGMIKRACEWDEWVVFTEREMVYRLRKLYPQKKFYPAREDAFCIGMKAITLKNIYESLKDMKYKVEVPEEIARKARKAIERMLEMSK

Source Source

Source organism organism	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,3-DIHYDROXYACETONEPHOSPHATE
Molecular weight formula_weight	170.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	522

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ktna1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.145 — NadA-like
Superfamily Superfamily superfamily	c.145.1 — NadA-like
Family Family family	c.145.1.1 — NadA-like

Domain ID domain_id	d5ktna2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	5ktnA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10800 — NadA-like

Domain ID domain_id	5ktnA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10800 — NadA-like

Domain ID domain_id	5ktnA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10800 — NadA-like

▶

Unit-cell length a length_a	47.303 Å
Unit-cell length b length_b	52.522 Å
Unit-cell length c length_c	55.544 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.340 Å
Low-resolution limit resolution_low	33.636 Å
R factor r_factor	0.1243
R_work r_work	0.1227
R_free r_free	0.1546

Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound dihydroxyacetone phosphate (DHAP) and Fe4S4 cluster

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

Quinolinate synthase A

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

5ktn__assembly_1__model_1

5ktn__assembly_1__model_1 | I(q)

5ktn__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound dihydroxyacetone phosphate (DHAP) and Fe4S4 cluster

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

Quinolinate synthase A

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

5ktn__assembly_1__model_1

5ktn__assembly_1__model_1 | I(q)

5ktn__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)