1s4p

Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor

Method: X-RAY DIFFRACTION

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

Glycolipid 2-alpha-mannosyltransferase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 methyl alpha-D-mannopyranoside × 2 MANGANESE (II) ION × 2 CHLORIDE ION × 4 GUANOSINE-5'-DIPHOSPHATE × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KRE2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–348； UniProt 97–442 Author chain B； PDBConstruct 3–348； UniProt 97–442

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	1s4p
Deposition date deposition_date	2004-01-16
Structure title title	Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor
Keywords keywords	;ALPHA/BETA FOLD, NUCLEOTIDE-BINDING DOMAIN, ROSSMANN FOLD, TERNARY COMPLEX WITH GDP-MN2+ AND METHYL-ALPHA-MANNOSIDE ACCEPTOR, 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.

1s4p__assembly_1__model_1

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

Download this curve (.dat)

1s4p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1s4p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.44 Å
Rg (electron density)	25.59 Å
Total Rg	26.46 Å
Atom count	5897
Residues	670
Excluded volume	104210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1s4p__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 (9)

Entity 1 Entity 1 polymer

Description description	Glycolipid 2-alpha-mannosyltransferase
Molecular weight formula_weight	41349.2 kDa
EC 编号 ec_number	2.4.1.131
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	6766

EFADAPIDTKTTMDYITPSFANKAGKPKACYVTLVRNKELKGLLSSIKYVENKINKKFPYPWVFLNDEPFTEEFKEAVTKAVSSEVKFGILPKEHWSYPEWINQTKAAEIRADAATKYIYGGSESYRHMCRYQSGFFWRHELLEEYDWYWRVEPDIKLYCDINYDVFKWMQENEKVYGFTVSIHEYEVTIPTLWQTSMDFIKKNPEYLDENNLMSFLSNDNGKTYNLCHFWSNFEIANLNLWRSPAYREYFDTLDHQGGFFYERWGDAPVHSIAAALFLPKDKIHYFSDIGYHHPPYDNCPLDKEVYNSNNCECDQGNDFTFQGYSCGKEYYDAQGLVKPKNWKKFRE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Pichia pastoris

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1397.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	methyl alpha-D-mannopyranoside
Molecular weight formula_weight	194.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	853

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1s4pa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.16 — Glycolipid 2-alpha-mannosyltransferase

Domain ID domain_id	d1s4pb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.16 — Glycolipid 2-alpha-mannosyltransferase

CATH v4.4 (2 domains)

Domain ID domain_id	1s4pA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	1s4pB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	60.694 Å
Unit-cell length b length_b	101.068 Å
Unit-cell length c length_c	62.036 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.81 °
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	2.010 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2560

Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor

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

Glycolipid 2-alpha-mannosyltransferase

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

1s4p__assembly_1__model_1

1s4p__assembly_1__model_1 | I(q)

1s4p__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor

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

Glycolipid 2-alpha-mannosyltransferase

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

1s4p__assembly_1__model_1

1s4p__assembly_1__model_1 | I(q)

1s4p__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)