1x9j

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes

Method: X-RAY DIFFRACTION

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

Probable butyrate kinase 2

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	GLYCEROL × 5 PHOSPHATE ION × 5 SODIUM ION × 1 CITRIC ACID × 4 water × 8	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 PHOSPHATE ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 2 PHOSPHATE ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 PHOSPHATE ION × 1 CITRIC ACID × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 PHOSPHATE ION × 2 SODIUM ION × 1 CITRIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BUK2_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 1–375 Author chain B； PDBConstruct 1–375； UniProt 1–375 Author chain C； PDBConstruct 1–375； UniProt 1–375 Author chain D； PDBConstruct 1–375； UniProt 1–375 Author chain E； PDBConstruct 1–375； UniProt 1–375 Author chain F； PDBConstruct 1–375； UniProt 1–375 Author chain G； PDBConstruct 1–375； UniProt 1–375 Author chain H； PDBConstruct 1–375； UniProt 1–375

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	1x9j
Deposition date deposition_date	2004-08-21
Structure title title	Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes
Keywords keywords	;ASKHA (ACETATE AND SUGAR KINASES, HSC70, ACTIN) SUPERFAMILY, BUTYRATE KINASE, ACETATE KINASE, ISOBUTYRATE KINASE, TWO SIMILAR DOMAINS, BUTYRATE, ISOBUTYRATE, ENZYME MECHANISM, 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.

1x9j__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1x9j__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1x9j__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	29.27 Å
Rg (electron density)	28.74 Å
Total Rg	29.37 Å
Atom count	5907
Residues	745
Excluded volume	105340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1x9j__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1x9j__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1x9j__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1x9j__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1x9j__assembly_5__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 (6)

Entity 1 Entity 1 polymer

Description description	Probable butyrate kinase 2
Molecular weight formula_weight	42083.4 kDa
EC 编号 ec_number	2.7.2.7
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	23615

MFRILTINPGSTSTKLSIFEDERMVKMQNFSHSPDELGRFQKILDQLEFREKIARQFVEETGYSLSSFSAFVSRGGLLDPIPGGVYLVDGLMIKTLKSGKNGEHASNLGAIIAHRFSSETGVPAYVVDPVVVDEMEDVARVSGHPNYQRKSIFHALNQKTVAKEVARMMNKRYEEMNLVVAHMGGGISIAAHRKGRVIDVNNALDGDGPFTPERSGTLPLTQLVDLCFSGKFTYEEMKKRIVGNGGLVAYLGTSDAREVVRRIKQGDEWAKRVYRAMAYQIAKWIGKMAAVLKGEVDFIVLTGGLAHEKEFLVPWITKRVSFIAPVLVFPGSNEEKALALSALRVLRGEEKPKNYSEESRRWRERYDSYLDGILR

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1x9ja1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9ja2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9je1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9je2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jg1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

Domain ID domain_id	d1x9jh2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.2 — Acetokinase-like

CATH v4.4 (16 domains)

Domain ID domain_id	1x9jA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1x9jH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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Unit-cell length a length_a	193.680 Å
Unit-cell length b length_b	193.680 Å
Unit-cell length c length_c	122.932 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	91.480 Å
R factor r_factor	—
R_work r_work	0.2610
R_free r_free	0.2840

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes

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

Probable butyrate kinase 2

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

1x9j__assembly_4__model_1

1x9j__assembly_4__model_1 | I(q)

1x9j__assembly_4__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (3)

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes

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

Probable butyrate kinase 2

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

1x9j__assembly_4__model_1

1x9j__assembly_4__model_1 | I(q)

1x9j__assembly_4__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (3)