7EY1 | pdb_00007ey1

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose

PDB DOI: https://doi.org/10.2210/pdb7EY1/pdb

Classification: HYDROLASE
Organism(s): Lentinula edodes
Expression System: Escherichia phage Ecwhy_1
Mutation(s): No

Deposited: 2021-05-29 Released: 2022-06-01
Deposition Author(s): Gong, W.M., Yang, L.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.249 (Depositor), 0.251 (DCC)
R-Value Work:
0.196 (Depositor), 0.203 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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: 359.67 kDa
Atom Count: 24,651
Modeled Residue Count: 3,024
Deposited Residue Count: 3,212
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, C, D	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: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	8	N/A	N/A	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth I], J [auth K], L [auth M]	3	N/A	N-Glycosylation	Interactions Focus chain H [auth I] Focus chain J [auth K] Focus chain L [auth M] Interactions & Density Focus chain H [auth I] Focus chain J [auth K] Focus chain L [auth M]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth J]	4	N/A	N/A	Interactions Focus chain I [auth J] Interactions & Density Focus chain I [auth J]

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(6-4)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth L]	8	N/A	N/A	Interactions Focus chain K [auth L] Interactions & Density Focus chain K [auth L]

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose	M [auth N]	2	N/A	N/A	Interactions Focus chain M [auth N] Interactions & Density Focus chain M [auth N]

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BKR (Subject of Investigation/LOI) Query on BKR Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain DA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain DA [auth B]	DA [auth B], U [auth A]	Deacetyltaxol C₄₅ H₄₉ N O₁₃ TYLVGQKNNUHXIP-MHHARFCSSA-N		Interactions Focus chain DA [auth B] Focus chain U [auth A] Interactions & Density Focus chain DA [auth B] Focus chain U [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain QA [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] GA [auth C] HA [auth C] AA [auth B], BA [auth B], CA [auth B], GA [auth C], HA [auth C], IA [auth C], KA [auth C], LA [auth C], MA [auth C], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], T [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain JA [auth C]	JA [auth C]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain JA [auth C] Interactions & Density Focus chain JA [auth C]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] MOL2 format, chain FA [auth B] mmCIF format, chain FA [auth B]	FA [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain FA [auth B] Interactions & Density Focus chain FA [auth B]
XYZ (Subject of Investigation/LOI) Query on XYZ Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain EA [auth B]	EA [auth B]	beta-D-xylofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-KKQCNMDGSA-N		Interactions Focus chain EA [auth B] Interactions & Density Focus chain EA [auth B]
XYP (Subject of Investigation/LOI) Query on XYP Download:Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.249 (Depositor), 0.251 (DCC)
R-Value Work: 0.196 (Depositor), 0.203 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 228.508	α = 90
b = 88.174	β = 90
c = 218.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Gong, W.M.

Yang, L.Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31270796

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 2.0: 2022-06-15
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-29
Changes: Data collection, Refinement description
Version 2.2: 2024-10-16
Changes: Structure summary