3POC | pdb_00003poc

The crystal structure of the D307A mutant of alpha-Glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with acarbose

PDB DOI: https://doi.org/10.2210/pdb3POC/pdb
Entry: 3POC supersedes: 3NQQ

Classification: hydrolase/hydrolase inhibitor
Organism(s): Blautia obeum ATCC 29174
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-11-22 Released: 2011-01-26
Deposition Author(s): Tan, K., Tesar, C., Wilton, R., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.225 (Depositor), 0.206 (DCC)
R-Value Work:
0.168 (Depositor)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The crystal structure of the D307A mutant of alpha-Glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with acarbose

Tan, K., Tesar, C., Wilton, R., Keigher, L., Babnigg, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 156.37 kDa
Atom Count: 11,497
Modeled Residue Count: 1,328
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-Glucosidase	A, B	666	Blautia obeum ATCC 29174	Mutation(s): 1 Gene Names: RUMOBE_03919 EC: 3.2.1
UniProt
Find proteins for A5ZY13 (Blautia obeum ATCC 29174) Explore A5ZY13 Go to UniProtKB: A5ZY13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5ZY13
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	3	N/A	N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G66431MI GlyCosmos: G66431MI

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AC1 Query on AC1 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose C₁₃ H₂₃ N O₈ RBZIIHWPZWOIDU-ZCGMLSCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
GLC Query on GLC 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]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007 Query on PRD_900007	C	alpha-acarbose	Oligosaccharide / Inhibitor		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.225 (Depositor), 0.206 (DCC)
R-Value Work: 0.168 (Depositor)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.954	α = 90
b = 125.691	β = 107.62
c = 87.968	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-01-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 3NQQ

Revision History (Full details and data files)

Version 1.0: 2011-01-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary