2PNC

Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine

PDB DOI: https://doi.org/10.2210/pdb2PNC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2007-04-24 Released: 2008-02-26
Deposition Author(s): Cendron, L., Holt, A., Smith, D.J., Zanotti, G., Rigo, A., Di Paolo, M.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252
R-Value Work: 0.237
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 168.01 kDa
Atom Count: 10,304
Modelled Residue Count: 1,246
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper amine oxidase, liver isozyme	A, B	746	Bos taurus	Mutation(s): 0 EC: 1.4.3.6
UniProt
Find proteins for Q29437 (Bos taurus) Explore Q29437 Go to UniProtKB: Q29437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q29437
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	C, D	3		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLU Query on CLU Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B]	I [auth A], O [auth B]	2,6-DICHLORO-N-IMIDAZOLIDIN-2-YLIDENEANILINE C₉ H₉ Cl₂ N₃ GJSURZIOUXUGAL-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B]	E [auth A], J [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	F [auth A], G [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	H [auth A], M [auth B], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPQ Query on TPQ	A, B	L-PEPTIDE LINKING	C₉ H₉ N O₅		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
CLU	Binding MOAD: 2PNC	Ki: 4.66e+5 (nM) from 1 assay(s)
CLU	PDBBind: 2PNC	Ki: 4.66e+5 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	C, D	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252
R-Value Work: 0.237
R-Value Observed: 0.238
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.36	α = 90
b = 131.956	β = 90
c = 134.159	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2012-07-25
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

2PNC

Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2