2j4l

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution

Method: X-RAY DIFFRACTION

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

URIDYLATE KINASE

SULFOLOBUS SOLFATARICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	;URIDINE 5'-TRIPHOSPHATE ; × 6 MAGNESIUM ION × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	;URIDINE 5'-TRIPHOSPHATE ; × 6 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRH_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–226； UniProt 2–227 Author chain B； PDBConstruct 1–226； UniProt 2–227 Author chain C； PDBConstruct 1–226； UniProt 2–227 Author chain D； PDBConstruct 1–226； UniProt 2–227 Author chain E； PDBConstruct 1–226； UniProt 2–227 Author chain F； PDBConstruct 1–226； UniProt 2–227 Author chain G； PDBConstruct 1–226； UniProt 2–227 Author chain H； PDBConstruct 1–226； UniProt 2–227 Author chain I； PDBConstruct 1–226； UniProt 2–227 Author chain J； PDBConstruct 1–226； UniProt 2–227 Author chain K； PDBConstruct 1–226； UniProt 2–227 Author chain L； PDBConstruct 1–226； UniProt 2–227

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	2j4l
Deposition date deposition_date	2006-09-01
Structure title title	Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution
Keywords keywords	UMP KINASE, NUCLEOSIDE MONOPHOSPHATE KINASE, PYRIMIDINE NUCLEOTIDE SYNTHESIS, ASPARTOKINASE FOLD, 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.

2j4l__assembly_1__model_1

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

Download this curve (.dat)

2j4l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j4l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.41 Å
Rg (electron density)	31.61 Å
Total Rg	32.40 Å
Atom count	10123
Residues	1274
Excluded volume	182320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j4l__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j4l__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	URIDYLATE KINASE
Molecular weight formula_weight	25016.9 kDa
EC 编号 ec_number	2.7.4.22
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	19613

MNIILKISGKFFDEDNVDNLIVLRQSIKELADNGFRVGIVTGGGSTARRYIKLAREIGIGEAYLDLLGIWASRLNAYLVMFSLQDLAYMHVPQSLEEFIQDWSHGKVVVTGGFQPGQSTAAVAALVAEASSSKTLVVATNVDGVYEKDPRIYADVKLIPHLTTQDLRKILEGSQSVQAGTYELLDPLAIKIVERSKIRVIVMNYRKLNRIIDILKGEEVSSIIEPV

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;URIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	484.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2j4la_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lb_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lc_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4ld_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4le_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lf_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lg_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lh_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4li_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lj_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4lk_
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.73.1.0 — automated matches

Domain ID domain_id	d2j4ll_
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.73.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2j4lA00
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	2j4lB00
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	2j4lC00
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	2j4lD00
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	2j4lE00
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	2j4lF00
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	2j4lG00
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	2j4lH00
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	2j4lI00
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	2j4lJ00
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	2j4lK00
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	2j4lL00
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

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Unit-cell length a length_a	224.750 Å
Unit-cell length b length_b	79.030 Å
Unit-cell length c length_c	223.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.630 Å
R factor r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.2780

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution

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

URIDYLATE KINASE

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

2j4l__assembly_1__model_1

2j4l__assembly_1__model_1 | I(q)

2j4l__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution

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

URIDYLATE KINASE

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

2j4l__assembly_1__model_1

2j4l__assembly_1__model_1 | I(q)

2j4l__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)