1G6I | pdb_00001g6i

Crystal structure of the yeast alpha-1,2-mannosidase with bound 1-deoxymannojirimycin at 1.59 A resolution

PDB DOI: https://doi.org/10.2210/pdb1G6I/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2000-11-06 Released: 2003-06-24
Deposition Author(s): Herscovics, A., Lipari, F., Sleno, B., Romera, P.A., Vallee, F., Yip, P., Howell, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.253 (Depositor)
R-Value Work:
0.230 (Depositor)
R-Value Observed:
0.230 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structure and function of Class I a1,2-mannosidases involved in glycoprotein biosynthesis.

Herscovics, A., Lipari, F., Sleno, B., Romera, P.A., Vallee, F., Yip, P., Howell, P.A.

(2002) Carbohydrate Bioengineering Interdisciplinary Approaches : 28-33

Macromolecule Content

Total Structure Weight: 65.2 kDa
Atom Count: 4,691
Modeled Residue Count: 510
Deposited Residue Count: 545
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS I ALPHA-1,2-MANNOSIDASE	A	545	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MNS1 EC: 3.2.1.113
UniProt
Find proteins for P32906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32906 Go to UniProtKB: P32906
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32906
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P32906-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation	Interactions Focus chain B
Glycosylation Resources
GlyTouCan: G34725OX GlyCosmos: G34725OX GlyGen: G34725OX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[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	C	5		N-Glycosylation	Interactions Focus chain C
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A]
DMJ Query on DMJ Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1-DEOXYMANNOJIRIMYCIN C₆ H₁₃ N O₄ LXBIFEVIBLOUGU-KVTDHHQDSA-N		Interactions Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.253 (Depositor)
R-Value Work: 0.230 (Depositor)
R-Value Observed: 0.230 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.052	α = 90
b = 89.052	β = 90
c = 153.142	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-06-24
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-02-08
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary