8JPZ | pdb_00008jpz

The thermostability mutant Gox_M8 from Aspergillus niger

PDB DOI: https://doi.org/10.2210/pdb8JPZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus niger
Expression System: Komagataella phaffii GS115
Mutation(s): No

Deposited: 2023-06-13 Released: 2023-12-20
Deposition Author(s): Tu, T., Yan, Y.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.204 (Depositor), 0.203 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (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

Revealing the intricate mechanism governing the pH-dependent activity of a quintessential representative of flavoproteins, glucose oxidase

Tu, T., Zhang, Y., Yan, Y., Li, L., Liu, X., Hakulinen, N., Zhang, W., Mu, Y., Luo, H., Yao, B., Li, W., Huang, H.

(2024) Fundam Res

DOI: https://doi.org/10.1016/j.fmre.2024.04.009

Macromolecule Content

Total Structure Weight: 133.12 kDa
Atom Count: 10,304
Modeled Residue Count: 1,162
Deposited Residue Count: 1,162
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose oxidase (Fragment)	A, B	581	Aspergillus niger	Mutation(s): 0 EC: 1.1.3.4
UniProt
Find proteins for Q5Q041 (Aspergillus niger) Explore Q5Q041 Go to UniProtKB: Q5Q041
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5Q041
Glycosylation
Glycosylation Sites: 7	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
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	C, D	6		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	E [auth A], N [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B]	F [auth A], O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
MPD (Subject of Investigation/LOI) Query on MPD Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A]	G [auth A], P [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]