3c1n

Crystal Structure of Allosteric Inhibition Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-threonine

Method: X-RAY DIFFRACTION

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

Probable aspartokinase

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	THREONINE × 7 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	THREONINE × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	THREONINE × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AK_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–473； UniProt 1–473 Author chain B； PDBConstruct 1–473； UniProt 1–473 Author chain C； PDBConstruct 1–473； UniProt 1–473 Author chain D； PDBConstruct 1–473； UniProt 1–473

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	3c1n
Deposition date deposition_date	2008-01-23
Structure title title	Crystal Structure of Allosteric Inhibition Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-threonine
Keywords keywords	kinase, allosteric inhibition, threonine-sensitive, ACT domain, Amino-acid biosynthesis, Threonine biosynthesis, Transferase; TRANSFERASE
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.

3c1n__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3c1n__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c1n__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	34.98 Å
Rg (electron density)	35.00 Å
Total Rg	35.26 Å
Atom count	6947
Residues	917
Excluded volume	125230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c1n__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c1n__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3c1n__assembly_3__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Probable aspartokinase
Molecular weight formula_weight	51457.1 kDa
EC 编号 ec_number	2.7.2.4
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	13893

MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKTNS

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	THREONINE
Molecular weight formula_weight	119.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3c1na1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d3c1na2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1na3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1nb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d3c1nb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1nb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1nc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d3c1nc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1nc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1nd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d3c1nd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

Domain ID domain_id	d3c1nd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3c1nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	3c1nA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	10 — VC0802-like

Domain ID domain_id	3c1nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	3c1nB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	10 — VC0802-like

Domain ID domain_id	3c1nC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	3c1nC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	10 — VC0802-like

Domain ID domain_id	3c1nD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	3c1nD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	10 — VC0802-like

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Unit-cell length a length_a	110.039 Å
Unit-cell length b length_b	144.317 Å
Unit-cell length c length_c	155.358 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2390
R_work r_work	0.2360
R_free r_free	0.2900

Crystal Structure of Allosteric Inhibition Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-threonine

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

Probable aspartokinase

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

3c1n__assembly_2__model_1

3c1n__assembly_2__model_1 | I(q)

3c1n__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Allosteric Inhibition Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-threonine

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

Probable aspartokinase

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

3c1n__assembly_2__model_1

3c1n__assembly_2__model_1 | I(q)

3c1n__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)