8GYY | pdb_00008gyy

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds

PDB DOI: https://doi.org/10.2210/pdb8GYY/pdb
Entry: 8GYY supersedes: 7F95

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

Deposited: 2022-09-24 Released: 2023-10-25
Deposition Author(s): Yang, L.Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.259 (Depositor), 0.268 (DCC)
R-Value Work:
0.219 (Depositor), 0.231 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose

Yang, L.Y.

To be published.

Macromolecule Content

Total Structure Weight: 363.14 kDa
Atom Count: 25,439
Modeled Residue Count: 3,025
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 [auth B], B [auth A], 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: 6	Glycosylation Focus chain A [auth B] Focus chain B [auth A] 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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, L, O, P	2		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain L Focus chain O Focus chain P Interactions & Density Focus chain E Focus chain H Focus chain L Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose	G	2		N/A	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G71689LT GlyCosmos: G71689LT GlyGen: G71689LT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

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

Entity ID: 7
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	K, M, N	3		N-Glycosylation	Interactions Focus chain K Focus chain M Focus chain N Interactions & Density Focus chain K Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 5 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 QA [auth A] SDF format, chain Q [auth B] SDF format, chain NB [auth D] SDF format, chain DB [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain DB [auth C] mmCIF format, chain QA [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain DB [auth C]	DB [auth C], NB [auth D], Q [auth B], QA [auth A]	Deacetyltaxol C₄₅ H₄₉ N O₁₃ TYLVGQKNNUHXIP-MHHARFCSSA-N		Interactions Focus chain DB [auth C] Focus chain NB [auth D] Focus chain Q [auth B] Focus chain QA [auth A] Interactions & Density Focus chain DB [auth C] Focus chain NB [auth D] Focus chain Q [auth B] Focus chain QA [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain JB [auth D] SDF format, chain LA [auth A] SDF format, chain PA [auth A] SDF format, chain X [auth B] SDF format, chain ZA [auth C] SDF format, chain Y [auth B] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain OA [auth A] SDF format, chain MB [auth D] SDF format, chain LB [auth D] SDF format, chain KB [auth D] SDF format, chain KA [auth A] SDF format, chain DA [auth B] SDF format, chain CB [auth C] SDF format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain KA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain LA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain X [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain LB [auth D] mmCIF format, chain KB [auth D] mmCIF format, chain KA [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth B]	AA [auth B] AB [auth C] BB [auth C] CA [auth B] CB [auth C] AA [auth B], AB [auth C], BB [auth C], CA [auth B], CB [auth C], DA [auth B], EA [auth B], FA [auth B], JB [auth D], KA [auth A], KB [auth D], LA [auth A], LB [auth D], MB [auth D], OA [auth A], PA [auth A], SA [auth C], TA [auth C], X [auth B], Y [auth B], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain ZA [auth C]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain EB [auth D] MOL2 format, chain EB [auth D] mmCIF format, chain EB [auth D]	EB [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain EB [auth D] Interactions & Density Focus chain EB [auth D]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain HB [auth D] SDF format, chain IA [auth A] SDF format, chain IB [auth D] SDF format, chain JA [auth A] SDF format, chain MA [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain Z [auth B] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain W [auth B] SDF format, chain UA [auth C] SDF format, chain U [auth B] SDF format, chain NA [auth A] SDF format, chain GB [auth D] SDF format, chain GA [auth A] SDF format, chain FB [auth D] SDF format, chain BA [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain JA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain BA [auth B]	BA [auth B] FB [auth D] GA [auth A] GB [auth D] HA [auth A] BA [auth B], FB [auth D], GA [auth A], GB [auth D], HA [auth A], HB [auth D], IA [auth A], IB [auth D], JA [auth A], MA [auth A], NA [auth A], S [auth B], T [auth B], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], WA [auth C], XA [auth C], YA [auth C], Z [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain BA [auth B] Focus chain FB [auth D] Focus chain GA [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth B] Focus chain FB [auth D] Focus chain GA [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B]
XLS (Subject of Investigation/LOI) Query on XLS Download:Ideal Coordinates CCD File SDF format, chain RA [auth A] SDF format, chain R [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain R [auth B] mmCIF format, chain RA [auth A] mmCIF format, chain R [auth B]	R [auth B], RA [auth A]	D-xylose C₅ H₁₀ O₅ PYMYPHUHKUWMLA-VPENINKCSA-N		Interactions Focus chain R [auth B] Focus chain RA [auth A] Interactions & Density Focus chain R [auth B] Focus chain RA [auth A]