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
View more details

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

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13006
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B [auth M]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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 MA [auth M] SDF format, chain N [auth A] MOL2 format, chain KA [auth M] MOL2 format, chain MA [auth M] MOL2 format, chain N [auth A] mmCIF format, chain KA [auth M] mmCIF format, chain MA [auth M] mmCIF format, chain N [auth A]	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 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 WA [auth M] SDF format, chain XA [auth M] SDF format, chain YA [auth M] SDF format, chain VA [auth M] SDF 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 WA [auth M] MOL2 format, chain XA [auth M] MOL2 format, chain YA [auth M] MOL2 format, chain VA [auth M] MOL2 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 WA [auth M] mmCIF format, chain XA [auth M] mmCIF format, chain YA [auth M] mmCIF format, chain VA [auth M] mmCIF format, chain AA [auth A]	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 JA [auth M] SDF format, chain L [auth A] SDF format, chain LA [auth M] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth M] MOL2 format, chain JA [auth M] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth M] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth M] mmCIF format, chain JA [auth M] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth M] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth M]	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 PA [auth M] SDF format, chain QA [auth M] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain OA [auth M] MOL2 format, chain PA [auth M] MOL2 format, chain QA [auth M] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth M] mmCIF format, chain PA [auth M] mmCIF format, chain QA [auth M] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth M]	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 X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth M] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth M] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [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]