8S1Z

Crystal structure of glycosylated human primary amine oxidase AOC3

PDB DOI: https://doi.org/10.2210/pdb8S1Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-02-16 Released: 2025-01-22
Deposition Author(s): Guedez, G., Alix, M., Salminen, T.A.
Funding Organization(s): Sigrid Juselius Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.320
R-Value Work: 0.286
R-Value Observed: 0.287

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

Structural flexibility of domains in human AOC3

Guedez, G., Alix, M., Salminen, T.A.

To be published.

Macromolecule Content

Total Structure Weight: 343.64 kDa
Atom Count: 23,705
Modelled Residue Count: 2,874
Deposited Residue Count: 2,948
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane primary amine oxidase	A, B, C, D	737	Homo sapiens	Mutation(s): 0 Gene Names: AOC3, VAP1 EC: 1.4.3.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q16853 (Homo sapiens) Explore Q16853 Go to UniProtKB: Q16853
PHAROS: Q16853 GTEx: ENSG00000131471
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16853
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q16853-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H, M, W	5		N-Glycosylation	Interactions Focus chain H Focus chain M Focus chain W Interactions & Density Focus chain H Focus chain M Focus chain W

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

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

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, V	2		N-Glycosylation	Interactions Focus chain L Focus chain V Interactions & Density Focus chain L Focus chain V

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	6		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P, U	3		N-Glycosylation	Interactions Focus chain P Focus chain U Interactions & Density Focus chain P Focus chain U

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	Q	4		N-Glycosylation	Interactions Focus chain Q Interactions & Density Focus chain Q

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	R	4		N-Glycosylation	Interactions Focus chain R Interactions & Density Focus chain R

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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	T	6		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T

Small Molecules

Ligands 3 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 EA [auth B] SDF format, chain FA [auth B] SDF format, chain MA [auth D] SDF format, chain NA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D]	AA [auth A], EA [auth B], FA [auth B], MA [auth D], NA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain MA [auth D] Focus chain NA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain MA [auth D] Focus chain NA [auth D]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain IA [auth C] SDF format, chain LA [auth D] SDF format, chain Z [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain Z [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain Z [auth A]	DA [auth B], IA [auth C], LA [auth D], Z [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain IA [auth C] Focus chain LA [auth D] Focus chain Z [auth A] Interactions & Density Focus chain DA [auth B] Focus chain IA [auth C] Focus chain LA [auth D] Focus chain Z [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	BA [auth B] CA [auth B] GA [auth C] HA [auth C] JA [auth D] BA [auth B], CA [auth B], GA [auth C], HA [auth C], JA [auth D], KA [auth D], X [auth A], Y [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain X [auth A] Focus chain Y [auth A]