1knx

HPr kinase/phosphatase from Mycoplasma pneumoniae

Method: X-RAY DIFFRACTION

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

Probable HPr(Ser) kinase/phosphatase

Mycoplasma pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HPRK_MYCPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 1–312 Author chain B； PDBConstruct 1–312； UniProt 1–312 Author chain C； PDBConstruct 1–312； UniProt 1–312 Author chain D； PDBConstruct 1–312； UniProt 1–312 Author chain E； PDBConstruct 1–312； UniProt 1–312 Author chain F； PDBConstruct 1–312； UniProt 1–312

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	1knx
Deposition date deposition_date	2001-12-19
Structure title title	HPr kinase/phosphatase from Mycoplasma pneumoniae
Keywords keywords	;HPr kinase, Hpr kinase/phosphatase, HPrK/P, kinase, phosphatase, P-loop, WALKER A BOX, CATABOLITE REPRESSION, transferase-hydrolase COMPLEX ;; transferase/hydrolase
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.

1knx__assembly_1__model_1

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

Download this curve (.dat)

1knx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1knx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.44 Å
Rg (electron density)	43.59 Å
Total Rg	43.68 Å
Atom count	14435
Residues	1827
Excluded volume	261750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1knx__assembly_1__model_1`	hexameric （6）	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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1knxa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.2 — HprK N-terminal domain-like
Family Family family	c.98.2.1 — HPr kinase/phoshatase HprK N-terminal domain

Domain ID domain_id	d1knxa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.2 — HPr kinase HprK C-terminal domain

Domain ID domain_id	d1knxb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.2 — HprK N-terminal domain-like
Family Family family	c.98.2.1 — HPr kinase/phoshatase HprK N-terminal domain

Domain ID domain_id	d1knxb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.2 — HPr kinase HprK C-terminal domain

Domain ID domain_id	d1knxc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.2 — HprK N-terminal domain-like
Family Family family	c.98.2.1 — HPr kinase/phoshatase HprK N-terminal domain

Domain ID domain_id	d1knxc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.2 — HPr kinase HprK C-terminal domain

Domain ID domain_id	d1knxd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.2 — HprK N-terminal domain-like
Family Family family	c.98.2.1 — HPr kinase/phoshatase HprK N-terminal domain

Domain ID domain_id	d1knxd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.2 — HPr kinase HprK C-terminal domain

Domain ID domain_id	d1knxe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.2 — HprK N-terminal domain-like
Family Family family	c.98.2.1 — HPr kinase/phoshatase HprK N-terminal domain

Domain ID domain_id	d1knxe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.2 — HPr kinase HprK C-terminal domain

Domain ID domain_id	d1knxf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.2 — HprK N-terminal domain-like
Family Family family	c.98.2.1 — HPr kinase/phoshatase HprK N-terminal domain

Domain ID domain_id	d1knxf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.2 — HPr kinase HprK C-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	1knxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — HprK N-terminal domain-like

Domain ID domain_id	1knxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1knxB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — HprK N-terminal domain-like

Domain ID domain_id	1knxB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1knxC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — HprK N-terminal domain-like

Domain ID domain_id	1knxC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1knxD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — HprK N-terminal domain-like

Domain ID domain_id	1knxD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1knxE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — HprK N-terminal domain-like

Domain ID domain_id	1knxE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1knxF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — HprK N-terminal domain-like

Domain ID domain_id	1knxF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	117.734 Å
Unit-cell length b length_b	127.845 Å
Unit-cell length c length_c	170.772 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	24

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.220 Å
R factor r_factor	0.2240
R_work r_work	0.2270
R_free r_free	0.2800

Description description	Probable HPr(Ser) kinase/phosphatase
Molecular weight formula_weight	35277.0 kDa
EC 编号 ec_number	2.7.1.-, 3.1.3.-
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14717

HPr kinase/phosphatase from Mycoplasma pneumoniae

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

Probable HPr(Ser) kinase/phosphatase

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

1knx__assembly_1__model_1

1knx__assembly_1__model_1 | I(q)

1knx__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Mycoplasma pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	2104
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	282

HPr kinase/phosphatase from Mycoplasma pneumoniae

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

Probable HPr(Ser) kinase/phosphatase

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

1knx__assembly_1__model_1

1knx__assembly_1__model_1 | I(q)

1knx__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)