9H7Z | pdb_00009h7z

Aspergillus niger Glucose Oxidase bound to Ba2+ ions

PDB DOI: https://doi.org/10.2210/pdb9H7Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus niger
Mutation(s): No

Deposited: 2024-10-28 Released: 2025-11-05
Deposition Author(s): Bauer, J.A., Bauerova, V.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.199 (Depositor), 0.197 (DCC)
R-Value Work:
0.177 (Depositor), 0.175 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Aspergillus niger Glucose Oxidase bound to Ba2+ ions

Bauer, J.A., Bauerova, V.

To be published.

Macromolecule Content

Total Structure Weight: 141.15 kDa
Atom Count: 10,144
Modeled Residue Count: 1,163
Deposited Residue Count: 1,210
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose oxidase	A, B [auth M]	605	Aspergillus niger	Mutation(s): 0 EC: 1.1.3.4
UniProt
Find proteins for P13006 (Aspergillus niger) Explore P13006 Go to UniProtKB: P13006
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13006
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B [auth M]
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)-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	C [auth B]	6		N-Glycosylation	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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 [auth C], E [auth D], F [auth E], H [auth I], I [auth U]	2		N-Glycosylation	Interactions Focus chain D [auth C] Focus chain E [auth D] Focus chain F [auth E] Focus chain H [auth I] Focus chain I [auth U] Interactions & Density Focus chain D [auth C] Focus chain E [auth D] Focus chain F [auth E] Focus chain H [auth I] Focus chain I [auth U]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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-(1-6)]beta-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	G [auth F]	8		N-Glycosylation	Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain NA [auth M] SDF format, chain O [auth A] MOL2 format, chain NA [auth M] MOL2 format, chain O [auth A] mmCIF format, chain NA [auth M] mmCIF format, chain O [auth A]	NA [auth M], O [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain NA [auth M] Focus chain O [auth A] Interactions & Density Focus chain NA [auth M] Focus chain O [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain KA [auth M] SDF format, chain N [auth A] SDF format, chain MA [auth M] MOL2 format, chain KA [auth M] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth M] mmCIF format, chain KA [auth M] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth M]	KA [auth M], MA [auth M], N [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain KA [auth M] Focus chain MA [auth M] Focus chain N [auth A] Interactions & Density Focus chain KA [auth M] Focus chain MA [auth M] Focus chain N [auth A]
MAN Query on MAN 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]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
BA Query on BA Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain TA [auth M] SDF format, chain UA [auth M] SDF format, chain VA [auth M] SDF format, chain WA [auth M] SDF format, chain XA [auth M] SDF format, chain YA [auth M] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain TA [auth M] MOL2 format, chain UA [auth M] MOL2 format, chain VA [auth M] MOL2 format, chain WA [auth M] MOL2 format, chain XA [auth M] MOL2 format, chain YA [auth M] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain TA [auth M] mmCIF format, chain UA [auth M] mmCIF format, chain VA [auth M] mmCIF format, chain WA [auth M] mmCIF format, chain XA [auth M] mmCIF format, chain YA [auth M]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], TA [auth M], UA [auth M], VA [auth M], WA [auth M], XA [auth M], YA [auth M]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain TA [auth M] Focus chain UA [auth M] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain YA [auth M] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain TA [auth M] Focus chain UA [auth M] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain YA [auth M]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain ZA [auth M] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain ZA [auth M] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain ZA [auth M]	GA [auth A], HA [auth A], ZA [auth M]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain ZA [auth M] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain ZA [auth M]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain IA [auth M] SDF format, chain JA [auth M] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth M] SDF format, chain J [auth A] MOL2 format, chain IA [auth M] MOL2 format, chain JA [auth M] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth M] MOL2 format, chain J [auth A] mmCIF format, chain IA [auth M] mmCIF format, chain JA [auth M] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth M] mmCIF format, chain J [auth A]	IA [auth M] J [auth A] JA [auth M] K [auth A] L [auth A] IA [auth M], J [auth A], JA [auth M], K [auth A], L [auth A], LA [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain IA [auth M] Focus chain J [auth A] Focus chain JA [auth M] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth M] Interactions & Density Focus chain IA [auth M] Focus chain J [auth A] Focus chain JA [auth M] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain OA [auth M] SDF format, chain PA [auth M] SDF format, chain Q [auth A] SDF format, chain QA [auth M] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain P [auth A] MOL2 format, chain OA [auth M] MOL2 format, chain PA [auth M] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth M] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain P [auth A] mmCIF format, chain OA [auth M] mmCIF format, chain PA [auth M] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth M] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain P [auth A]	OA [auth M] P [auth A] PA [auth M] Q [auth A] QA [auth M] OA [auth M], P [auth A], PA [auth M], Q [auth A], QA [auth M], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain OA [auth M] Focus chain P [auth A] Focus chain PA [auth M] Focus chain Q [auth A] Focus chain QA [auth M] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain OA [auth M] Focus chain P [auth A] Focus chain PA [auth M] Focus chain Q [auth A] Focus chain QA [auth M] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain RA [auth M] SDF format, chain SA [auth M] SDF format, chain W [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain X [auth A] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth M] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain X [auth A] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth M] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain X [auth A]	RA [auth M] SA [auth M] W [auth A] X [auth A] Y [auth A] RA [auth M], SA [auth M], W [auth A], X [auth A], Y [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain RA [auth M] Focus chain SA [auth M] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain RA [auth M] Focus chain SA [auth M] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]