7EY2 | pdb_00007ey2

Bifunctional xylosidase/glucosidase LXYL D300N mutant with intermediate substrate xylose

PDB DOI: https://doi.org/10.2210/pdb7EY2/pdb

Classification: HYDROLASE
Organism(s): Lentinula edodes
Expression System: Escherichia coli
Mutation(s): Yes

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: 2.43 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (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: 540.68 kDa
Atom Count: 37,142
Modeled Residue Count: 4,542
Deposited Residue Count: 4,830
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-D-xylosidase/beta-D-glucosidase	A, B, C, D, E A, B, C, D, E, F	805	Lentinula edodes	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G8GLP2
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J, M, P, S G, J, M, P, S, V	3		N-Glycosylation	Interactions Focus chain G Focus chain J Focus chain M Focus chain P Focus chain S Focus chain V Interactions & Density Focus chain G Focus chain J Focus chain M Focus chain P Focus chain S Focus chain V
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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	H, N, T, W	7		N-Glycosylation	Interactions Focus chain H Focus chain N Focus chain T Focus chain W Interactions & Density Focus chain H Focus chain N Focus chain T Focus chain W
Glycosylation Resources
GlyTouCan: G90815BM GlyCosmos: G90815BM GlyGen: G90815BM

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, R	5		N-Glycosylation	Interactions Focus chain I Focus chain R Interactions & Density Focus chain I Focus chain R
Glycosylation Resources
GlyTouCan: G75436UI GlyCosmos: G75436UI GlyGen: G75436UI

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	8		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, O, U, X	6		N-Glycosylation	Interactions Focus chain L Focus chain O Focus chain U Focus chain X Interactions & Density Focus chain L Focus chain O Focus chain U Focus chain X
Glycosylation Resources
GlyTouCan: G60005GQ GlyCosmos: G60005GQ GlyGen: G60005GQ

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q	6		N/A	Interactions Focus chain Q Interactions & Density Focus chain Q

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain IA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain Y [auth A] SDF format, chain YA [auth F] SDF format, chain Z [auth A] SDF format, chain ZA [auth F] SDF format, chain XA [auth F] SDF format, chain JA [auth C] SDF format, chain EA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain JA [auth C] MOL2 format, chain EA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain JA [auth C] mmCIF format, chain EA [auth B]	AA [auth A] BA [auth A] EA [auth B] FA [auth B] GA [auth B] AA [auth A], BA [auth A], EA [auth B], FA [auth B], GA [auth B], IA [auth C], JA [auth C], KA [auth C], LA [auth C], NA [auth D], OA [auth D], PA [auth D], QA [auth D], RA [auth D], TA [auth E], UA [auth E], VA [auth E], XA [auth F], Y [auth A], YA [auth F], Z [auth A], ZA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain XA [auth F] Focus chain Y [auth A] Focus chain YA [auth F] Focus chain Z [auth A] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain XA [auth F] Focus chain Y [auth A] Focus chain YA [auth F] Focus chain Z [auth A] Focus chain ZA [auth F]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain DA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain DA [auth A]	DA [auth A]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]
XYL (Subject of Investigation/LOI) Query on XYL Download Ideal Coordinates CCD File SDF format, chain WA [auth E] SDF format, chain SA [auth D] SDF format, chain MA [auth C] MOL2 format, chain WA [auth E] MOL2 format, chain SA [auth D] MOL2 format, chain MA [auth C] mmCIF format, chain WA [auth E] mmCIF format, chain SA [auth D] mmCIF format, chain MA [auth C]	MA [auth C], SA [auth D], WA [auth E]	Xylitol C₅ H₁₂ O₅ HEBKCHPVOIAQTA-SCDXWVJYSA-N		Interactions Focus chain MA [auth C] Focus chain SA [auth D] Focus chain WA [auth E] Interactions & Density Focus chain MA [auth C] Focus chain SA [auth D] Focus chain WA [auth E]
XYZ (Subject of Investigation/LOI) Query on XYZ Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain HA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain HA [auth B]	CA [auth A], HA [auth B]	beta-D-xylofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-KKQCNMDGSA-N		Interactions Focus chain CA [auth A] Focus chain HA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain HA [auth B]