8KAP | pdb_00008kap

Glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus (ligand-free)

PDB DOI: https://doi.org/10.2210/pdb8KAP/pdb

Classification: HYDROLASE
Organism(s): Streptomyces griseus subsp. griseus NBRC 13350
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.232 (Depositor), 0.240 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 184.74 kDa
Atom Count: 12,655
Modeled Residue Count: 1,574
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SGR_2426	A, B, C, D	414	Streptomyces griseus subsp. griseus NBRC 13350	Mutation(s): 0 EC: 3.2.1.21
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
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], J [auth C], K [auth C], M [auth D]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain L [auth D]	G [auth B], L [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]