7YO7 | pdb_00007yo7

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 5 seconds

PDB DOI: https://doi.org/10.2210/pdb7YO7/pdb

Classification: HYDROLASE
Organism(s): Lentinula edodes
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2022-08-01 Released: 2023-08-09
Deposition Author(s): Yang, L.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.250 (Depositor), 0.254 (DCC)
R-Value Work:
0.212 (Depositor), 0.219 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose

Gong, W.M., Yang, L.Y.

To be published.

Macromolecule Content

Total Structure Weight: 179 kDa
Atom Count: 12,859
Modeled Residue Count: 1,513
Deposited Residue Count: 1,606
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-D-xylosidase/beta-D-glucosidase	A, B	803	Lentinula edodes	Mutation(s): 0 Gene Names: Lxyl-p1-2 EC: 3.2.1.21
UniProt
Find proteins for G8GLP2 (Lentinula edodes) Explore G8GLP2 Go to UniProtKB: G8GLP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8GLP2
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-1)-alpha-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4	N/A	N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G, H, I, J	2	N/A	N-Glycosylation	Interactions Focus chain D Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain D Focus chain G Focus chain H Focus chain I Focus chain J

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose	E, F	2	N/A	N/A	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BKR Query on BKR Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B]	M [auth A], S [auth B]	Deacetyltaxol C₄₅ H₄₉ N O₁₃ TYLVGQKNNUHXIP-MHHARFCSSA-N		Interactions Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain S [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	K [auth A] L [auth A] O [auth A] P [auth A] Q [auth B] K [auth A], L [auth A], O [auth A], P [auth A], Q [auth B], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B]
XLS (Subject of Investigation/LOI) Query on XLS Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B]	N [auth A], T [auth B]	D-xylose C₅ H₁₀ O₅ PYMYPHUHKUWMLA-VPENINKCSA-N		Interactions Focus chain N [auth A] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain T [auth B]