2f3t

Crystal Structure Of E.coli Guanylate Kinase In Complex With Ganciclovir monophosphate

Method: X-RAY DIFFRACTION

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

Guanylate kinase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	N9-1-HYDROXY-PROP-2-OXYMETHYL-GUANINE-3'-MONOPHOSPHATE × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KGUA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 1–207 Author chain B； PDBConstruct 1–207； UniProt 1–207 Author chain C； PDBConstruct 1–207； UniProt 1–207 Author chain D； PDBConstruct 1–207； UniProt 1–207 Author chain E； PDBConstruct 1–207； UniProt 1–207 Author chain F； PDBConstruct 1–207； UniProt 1–207

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	2f3t
Deposition date deposition_date	2005-11-22
Structure title title	Crystal Structure Of E.coli Guanylate Kinase In Complex With Ganciclovir monophosphate
Keywords keywords	TRANSFERASE, GMP KINASE, GUANYLATE KINASE, NUCLEOTIDE ANALOGUE; 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.

2f3t__assembly_1__model_1

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

Download this curve (.dat)

2f3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f3t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.99 Å
Rg (electron density)	32.76 Å
Total Rg	33.31 Å
Atom count	9900
Residues	1223
Excluded volume	174680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f3t__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 (3)

Entity 1 Entity 1 polymer

Description description	Guanylate kinase
Molecular weight formula_weight	23625.7 kDa
EC 编号 ec_number	2.7.4.8
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9925

MAQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLAD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N9-1-HYDROXY-PROP-2-OXYMETHYL-GUANINE-3'-MONOPHOSPHATE
Molecular weight formula_weight	335.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2f3ta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d2f3tb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d2f3tc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d2f3td_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d2f3te_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d2f3tf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

CATH v4.4 (12 domains)

Domain ID domain_id	2f3tA01
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	2f3tA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

Domain ID domain_id	2f3tB01
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	2f3tB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

Domain ID domain_id	2f3tC01
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	2f3tC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

Domain ID domain_id	2f3tD01
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	2f3tD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

Domain ID domain_id	2f3tE01
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	2f3tE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

Domain ID domain_id	2f3tF01
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	2f3tF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

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Unit-cell length a length_a	107.753 Å
Unit-cell length b length_b	107.753 Å
Unit-cell length c length_c	272.663 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	48

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.160 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2680
R_work r_work	0.2680
R_free r_free	0.2900

Crystal Structure Of E.coli Guanylate Kinase In Complex With Ganciclovir monophosphate

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

Guanylate 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

2f3t__assembly_1__model_1

2f3t__assembly_1__model_1 | I(q)

2f3t__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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure Of E.coli Guanylate Kinase In Complex With Ganciclovir monophosphate

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

Guanylate 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

2f3t__assembly_1__model_1

2f3t__assembly_1__model_1 | I(q)

2f3t__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 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)