6ZJ1

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with tetrasaccharide N-glycan fragment and hexatungstotellurate(VI) TEW

PDB DOI: https://doi.org/10.2210/pdb6ZJ1/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-06-27 Released: 2020-12-02
Deposition Author(s): Sobala, L.F., Fernandes, P.Z., Hakki, Z., Thompson, A.J., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.
Funding Organization(s): European Research Council (ERC), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.252
R-Value Work: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 48.72 kDa
Atom Count: 3,273
Modelled Residue Count: 362
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein endo-alpha-1,2-mannosidase	A [auth AAA]	382	Homo sapiens	Mutation(s): 1 Gene Names: MANEA EC: 3.2.1.130
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SRI9 (Homo sapiens) Explore Q5SRI9 Go to UniProtKB: Q5SRI9
PHAROS: Q5SRI9 GTEx: ENSG00000172469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SRI9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranoside	B [auth AdA]	4		N/A	Interactions Focus chain B [auth AdA] Interactions & Density Focus chain B [auth AdA]
Glycosylation Resources
GlyTouCan: G58365BL GlyCosmos: G58365BL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TEW Query on TEW Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA]	D [auth AAA], E [auth AAA]	6-tungstotellurate(VI) O₂₄ Te W₆ JDLYBIMRCSJRQJ-UHFFFAOYSA-M		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA]	C [auth AAA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.252
R-Value Work: 0.184
Space Group: P 6₂
Diffraction Data: https://doi.org/10.5281/zenodo.4288341

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.414	α = 90
b = 129.414	β = 90
c = 50.201	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
STARANISO	data processing
REFMAC	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	322942
Australian Research Council (ARC)	Australia	DP120101396
Australian Research Council (ARC)	Australia	FT130100103
Australian Research Council (ARC)	Australia	DP180101957

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2020-12-09
Changes: Database references
Version 1.2: 2021-01-20
Changes: Database references
Version 1.3: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description