3HN3 | pdb_00003hn3

Human beta-glucuronidase at 1.7 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HN3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Mus musculus
Mutation(s): No

Deposited: 2009-05-29 Released: 2009-12-01
Deposition Author(s): Klei, H.E., Ghosh, K., Anumula, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.240 (Depositor)
R-Value Work:
0.203 (Depositor), 0.211 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human beta-glucuronidasel at 1.7 A resolution

Klei, H.E., Ghosh, K., Anumula, R.

To be published.

Macromolecule Content

Total Structure Weight: 291.59 kDa
Atom Count: 23,390
Modeled Residue Count: 2,430
Deposited Residue Count: 2,452
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucuronidase	A, B, C [auth D], D [auth E]	613	Homo sapiens	Mutation(s): 0 Gene Names: PLACENTAL GUS EC: 3.2.1.31
UniProt & NIH Common Fund Data Resources
Find proteins for P08236 (Homo sapiens) Explore P08236 Go to UniProtKB: P08236
PHAROS: P08236 GTEx: ENSG00000169919
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08236
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C [auth D] Focus chain D [auth E]	Go to GlyGen: P08236-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-L-gulopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	10		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G64020XR GlyCosmos: G64020XR GlyGen: G64020XR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	10		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G20212GT GlyCosmos: G20212GT GlyGen: G20212GT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	10		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G89864BN GlyCosmos: G89864BN GlyGen: G89864BN

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	H	10		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

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 I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth D] SDF format, chain O [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E]	I [auth A], K [auth B], M [auth D], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth D] Focus chain O [auth E]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E] mmCIF format, chain P [auth E]	P [auth E]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth E] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth E] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth E]	L [auth B], Q [auth E]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain L [auth B] Focus chain Q [auth E] Interactions & Density Focus chain L [auth B] Focus chain Q [auth E]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain N [auth D] SDF format, chain J [auth A] MOL2 format, chain R [auth E] MOL2 format, chain N [auth D] MOL2 format, chain J [auth A] mmCIF format, chain R [auth E] mmCIF format, chain N [auth D] mmCIF format, chain J [auth A]	J [auth A], N [auth D], R [auth E]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain J [auth A] Focus chain N [auth D] Focus chain R [auth E] Interactions & Density Focus chain J [auth A] Focus chain N [auth D] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.240 (Depositor)
R-Value Work: 0.203 (Depositor), 0.211 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.578	α = 90
b = 123.115	β = 90
c = 266.135	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

Klei, H.E.

Ghosh, K.

Anumula, R.

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-04
Changes: Advisory, Data collection, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-10-16
Changes: Advisory, Data collection, Database references, Structure summary