4DO5

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

PDB DOI: https://doi.org/10.2210/pdb4DO5/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2012-02-09 Released: 2012-10-10
Deposition Author(s): Clark, N.E., Garman, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.178
R-Value Work: 0.159
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 96.28 kDa
Atom Count: 7,745
Modelled Residue Count: 787
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-N-acetylgalactosaminidase	A, B	400	Homo sapiens	Mutation(s): 1 Gene Names: NAGA EC: 3.2.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P17050 (Homo sapiens) Explore P17050 Go to UniProtKB: P17050
PHAROS: P17050 GTEx: ENSG00000198951
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17050
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	D, F	5		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth B]	G [auth A], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain R [auth B]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B]	I [auth A], T [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain T [auth B]
DGJ Query on DGJ Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B]	H [auth A], S [auth B]	(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol C₆ H₁₃ N O₄ LXBIFEVIBLOUGU-DPYQTVNSSA-N		Interactions Focus chain H [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
DGJ	PDBBind: 4DO5	Ki: 1480 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.178
R-Value Work: 0.159
R-Value Observed: 0.160
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.352	α = 90
b = 114.513	β = 95.64
c = 68.553	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Clark, N.E.

Garman, S.C.

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-11-21
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4DO5

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources