SAXSdb — 2yk4

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

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE

NEISSERIA MENINGITIDIS SEROGROUP B

UniProt P72097

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL ; × 2 1,2-ETHANEDIOL × 6 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LST_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–323； UniProt 49–370

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	2yk4
Deposition date deposition_date	2011-05-25
Structure title title	Structure of Neisseria LOS-specific sialyltransferase (NST).
Keywords keywords	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.

2yk4__assembly_1__model_1

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

Download this curve (.dat)

2yk4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yk4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.18 Å
Rg (electron density)	29.54 Å
Total Rg	29.88 Å
Atom count	5402
Residues	630
Excluded volume	97933 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yk4__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 (5)

Entity 1 Entity 1 polymer

Description description	CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE
Molecular weight formula_weight	38210.2 kDa
EC 编号 ec_number	2.4.99.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2954

EPVNLIFCYTILQMKVAERIMAQHPGERFYVVLMSENRNEKYDYYFNQIKDKAEWAYFFHLPYGLNKSFNFIPTMAELKVKAMLLPKVKRIYLASLEKVSIAAFLSTYPDAEIKTFDDGTINLIQSSSYLGDEFSVNGTIKRNFARMMIGDWSIAKTRNASDEHYTIFKGLKNIMDDGRRKMTYLPLFDASELKAGDETGGTVRILLGSPDKEMKEISEKAAKNFNIQYVAPHPRQTYGLSGVTTLNSPYVIEDYILREIKKNPHTRYEIYTFFSGAALTMKDFPNVHVYALKPASLPEDYWLKPVYALFTQSGIPILTFDDKLVPR

Source Source

Source organism organism	NEISSERIA MENINGITIDIS SEROGROUP B
NCBI taxonomy ID ncbi_taxonomy_id	491
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL ;
Molecular weight formula_weight	602.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2yk4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	86.565 Å
Unit-cell length b length_b	124.735 Å
Unit-cell length c length_c	41.866 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	71.070 Å
R factor r_factor	0.1964
R_work r_work	0.1950
R_free r_free	0.2227

Structure of Neisseria LOS-specific sialyltransferase (NST).

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

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE

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

2yk4__assembly_1__model_1

2yk4__assembly_1__model_1 | I(q)

2yk4__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of Neisseria LOS-specific sialyltransferase (NST).

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

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE

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

2yk4__assembly_1__model_1

2yk4__assembly_1__model_1 | I(q)

2yk4__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)