SAXSdb — 3cwc

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

Putative glycerate kinase 2

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZME0_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–383； UniProt 1–380 Author chain B； PDBConstruct 4–383； UniProt 1–380

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	3cwc
Deposition date deposition_date	2008-04-21
Structure title title	Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2
Keywords keywords	structural genomics, Center for Structural Genomics of Infectious Diseases, CSGID, IDP122, Kinase, 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.

3cwc__assembly_1__model_1

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

Download this curve (.dat)

3cwc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cwc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.88 Å
Rg (electron density)	36.84 Å
Total Rg	36.89 Å
Atom count	5414
Residues	729
Excluded volume	96308 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cwc__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Putative glycerate kinase 2
Molecular weight formula_weight	40152.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5567

SNAMKIVIAPDSYKESLSALEVATAIEQGFREIWPDADYLKLPLADGGEGTVEAMVEATAGRIVHVEVTGPLGHRVNAFYGLSGDARSAFIEMAAASGLEQVPPAQRDPLKTTSWGTGELIRHALDAGVEHIIIGIGGSATNDGGAGMVQALGARLRDAQGNDIAQGGIGLETLASIDISGLDKRLSACHIEVACDVTNPLTGKEGASAVFGPQKGATPEMIERLDTALTRYAHLIARDLHVDVLDLAGGGAAGGMGAALYAFCGAQLRRGIEIVTDALHLEACLADADLVITGEGRIDSQTIHGKVPIGVANIAKRYNKPVIGIAGSLTADVSVVHEHGLDAVFSVIYTICTLEDALKNASENVRMTARNVAATLKAGQQLR

Source Source

Source organism organism	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Common name common_name	Salmonella typhimurium LT2
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3cwca1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.141 — Glycerate kinase I
Superfamily Superfamily superfamily	c.141.1 — Glycerate kinase I
Family Family family	c.141.1.0 — automated matches

Domain ID domain_id	d3cwca2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cwcb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.141 — Glycerate kinase I
Superfamily Superfamily superfamily	c.141.1 — Glycerate kinase I
Family Family family	c.141.1.0 — automated matches

Domain ID domain_id	d3cwcb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3cwcA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10350 — Glycerate kinase; domain 1

Domain ID domain_id	3cwcA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1510 — Glycerate kinase, domain 2
Homologous superfamily homologous superfamily	10 — Glycerate kinase, domain 2

Domain ID domain_id	3cwcB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10350 — Glycerate kinase; domain 1

Domain ID domain_id	3cwcB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1510 — Glycerate kinase, domain 2
Homologous superfamily homologous superfamily	10 — Glycerate kinase, domain 2

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Unit-cell length a length_a	63.733 Å
Unit-cell length b length_b	59.549 Å
Unit-cell length c length_c	103.605 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.230 Å
Low-resolution limit resolution_low	49.810 Å
R factor r_factor	0.1910
R_work r_work	0.1880
R_free r_free	0.2370

Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2

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

Putative glycerate 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

3cwc__assembly_1__model_1

3cwc__assembly_1__model_1 | I(q)

3cwc__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2

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

Putative glycerate 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

3cwc__assembly_1__model_1

3cwc__assembly_1__model_1 | I(q)

3cwc__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)