SAXSdb — 1to6

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

Glycerate kinase

Neisseria meningitidis serogroup A

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 12 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLXK_NEIMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–371； UniProt 1–371 Author chain B； PDBConstruct 1–371； UniProt 1–371

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	1to6
Deposition date deposition_date	2004-06-13
Structure title title	Glycerate kinase from Neisseria meningitidis (serogroup A)
Keywords keywords	;GLYCERATE METABOLISM, STRUCTURAL GENOMICS T831, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, 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.

1to6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1to6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1to6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	37.13 Å
Rg (electron density)	36.46 Å
Total Rg	36.86 Å
Atom count	11164
Residues	1484
Excluded volume	199570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1to6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1to6__assembly_2__model_1`	tetrameric （4）	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	Glycerate kinase
Molecular weight formula_weight	39565.1 kDa
EC 编号 ec_number	2.7.1.31
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	5777

MKIVIAPDSFKESLTAQQVAEAIKRGFQQSIADVECLLCPVGDGGEGTVDAIRHSLDLEEKCLQVTGSFGQKEVMRYFQKEQLALFEVADLVGLGKIPLEKRNPLQIQTRGIGELIRHLISQEIKEIYIGVGGTASNDGGIGIAAGLGYQFYDEDGNALPACGQSLLNLASVSTENRYKIPEDVHIRILADVVSPLCGHQGATYTFGKQKGLDSTMFEVVDQAIQDFYEKVSPATLKLKGAGAGGGIAGGLCAFAQASIVSGIDTCLDLIDFDKKVSDVDLVIVGEGRLDRQSLAGKAPIGVAKRTPVGVPVVAICGSLVEDLPSLPFENIQAAFSILEKSEPLEDSLKNASLYLEHTASNIGHLLNMPKI

Source Source

Source organism organism	Neisseria meningitidis serogroup A
NCBI taxonomy ID ncbi_taxonomy_id	65699
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	195

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1to6a_
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.141.1.1 — Glycerate kinase I

Domain ID domain_id	d1to6b_
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.141.1.1 — Glycerate kinase I

CATH v4.4 (4 domains)

Domain ID domain_id	1to6A01
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	1to6A02
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	1to6B01
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	1to6B02
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	105.767 Å
Unit-cell length b length_b	77.386 Å
Unit-cell length c length_c	101.436 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.760 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2830

Glycerate kinase from Neisseria meningitidis (serogroup A)

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

Glycerate 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

1to6__assembly_2__model_1

1to6__assembly_2__model_1 | I(q)

1to6__assembly_2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Glycerate kinase from Neisseria meningitidis (serogroup A)

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

Glycerate 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

1to6__assembly_2__model_1

1to6__assembly_2__model_1 | I(q)

1to6__assembly_2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)