8KAQ

Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from Streptomyces griseus (sophorose complex)

PDB DOI: https://doi.org/10.2210/pdb8KAQ/pdb

Classification: HYDROLASE
Organism(s): Streptomyces griseus subsp. griseus NBRC 13350
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-08-03 Released: 2024-08-07
Deposition Author(s): Kumakura, H., Motouchi, S., Nakai, H., Nakajima, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.223
R-Value Work: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Identification of beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus

Kumakura, H., Motouchi, S., Nakai, H., Nakajima, M.

To be published.

Macromolecule Content

Total Structure Weight: 185.41 kDa
Atom Count: 12,837
Modelled Residue Count: 1,560
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative beta-glucosidase	A, B, C, D	414	Streptomyces griseus subsp. griseus NBRC 13350	Mutation(s): 1 Gene Names: SGR_2426
UniProt
Find proteins for B1W1N0 (Streptomyces griseus subsp. griseus (strain JCM 4626 / CBS 651.72 / NBRC 13350 / KCC S-0626 / ISP 5235)) Explore B1W1N0 Go to UniProtKB: B1W1N0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1W1N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC (Subject of Investigation/LOI) Query on GLC Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth C]	I [auth A], L [auth B], U [auth C]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain U [auth C]
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	E [auth A] F [auth A] H [auth A] M [auth B] Q [auth C] E [auth A], F [auth A], H [auth A], M [auth B], Q [auth C], R [auth C], T [auth C], W [auth D]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth C] Focus chain W [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C]	G [auth A], N [auth B], S [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain S [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D]	J [auth A] K [auth A] O [auth B] P [auth B] V [auth C] J [auth A], K [auth A], O [auth B], P [auth B], V [auth C], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain X [auth D]