7JJN | pdb_00007jjn

Eubacterium rectale Amy13B (EUR_01860)

PDB DOI: https://doi.org/10.2210/pdb7JJN/pdb

Classification: HYDROLASE
Organism(s): Agathobacter rectalis DSM 17629
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-07-27 Released: 2021-06-23
Deposition Author(s): Koropatkin, N.M., Cockburn, D.W., Cerqueira, F.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.198 (Depositor), 0.179 (DCC)
R-Value Work:
0.162 (Depositor)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structures of the GH13_36 amylases from Eubacterium rectale and Ruminococcus bromii reveal subsite architectures that favor maltose production

Cockburn, D.W., Cerqueira, F.M., Bahr, C.M.E., Koropatkin, N.M.

(2020) Amylase 4: 24-44

DOI: https://doi.org/10.1515/amylase-2020-0003

Macromolecule Content

Total Structure Weight: 120.37 kDa
Atom Count: 8,787
Modeled Residue Count: 1,023
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosidases	A, B	526	Agathobacter rectalis DSM 17629	Mutation(s): 3 Gene Names: EUR_01860 EC: 3.2.1.1

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	C [auth D], D [auth E]	3		N/A	Interactions Focus chain C [auth D] Focus chain D [auth E] Interactions & Density Focus chain C [auth D] Focus chain D [auth E]
Glycosylation Resources
GlyTouCan: G00395FS GlyCosmos: G00395FS GlyGen: G00395FS

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900065 Query on PRD_900065	C [auth D], D [auth E]	beta-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain C [auth D] Focus chain D [auth E] Interactions & Density Focus chain C [auth D] Focus chain D [auth E]