4Z10

Inactive aurone synthase (polyphenol oxidase) co-crystallized with 1,4-resorcinol

PDB DOI: https://doi.org/10.2210/pdb4Z10/pdb

Classification: OXIDOREDUCTASE
Organism(s): Coreopsis grandiflora
Mutation(s): No

Deposited: 2015-03-26 Released: 2016-04-06
Deposition Author(s): Molitor, C., Mauracher, S.G., Rompel, A.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.179
R-Value Work: 0.144
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Inactive aurone synthase (polyphenol oxidase) co-crystallized with 1,4-resorcinol

Molitor, C., Mauracher, S.G., Rompel, A.

To be published.

Macromolecule Content

Total Structure Weight: 252.49 kDa
Atom Count: 18,768
Modelled Residue Count: 2,131
Deposited Residue Count: 2,190
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurone synthase	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	350	Coreopsis grandiflora	Mutation(s): 0
UniProt
Find proteins for A0A075DN54 (Coreopsis grandiflora) Explore A0A075DN54 Go to UniProtKB: A0A075DN54
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A075DN54
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurone synthase	B [auth G] D [auth H] F [auth I] H [auth J] J [auth K] B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	15	Coreopsis grandiflora	Mutation(s): 0
UniProt
Find proteins for A0A075DN54 (Coreopsis grandiflora) Explore A0A075DN54 Go to UniProtKB: A0A075DN54
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A075DN54
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RCO Query on RCO Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	DA [auth D] EA [auth D] HA [auth E] IA [auth E] N [auth A] DA [auth D], EA [auth D], HA [auth E], IA [auth E], N [auth A], O [auth A], P [auth A], S [auth B], T [auth B], Y [auth C], Z [auth C]	RESORCINOL C₆ H₆ O₂ GHMLBKRAJCXXBS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	AA [auth C] BA [auth C] FA [auth D] Q [auth A] U [auth B] AA [auth C], BA [auth C], FA [auth D], Q [auth A], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain KA [auth F] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C]	CA [auth D] GA [auth E] KA [auth F] M [auth A] R [auth B] CA [auth D], GA [auth E], KA [auth F], M [auth A], R [auth B], X [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain X [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain JA [auth K] MOL2 format, chain JA [auth K]	JA [auth K]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain JA [auth K] Interactions & Density Focus chain JA [auth K]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HS8 Query on HS8	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	L-PEPTIDE LINKING	C₆ H₁₀ N₃ O₅ S		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.179
R-Value Work: 0.144
R-Value Observed: 0.146
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.1	α = 90
b = 137.1	β = 90
c = 209.52	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Molitor, C.

Mauracher, S.G.

Rompel, A.

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P25217-N28

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2018-11-21
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description