3ZK4

Structure of purple acid phosphatase PPD1 isolated from yellow lupin (Lupinus luteus) seeds

PDB DOI: https://doi.org/10.2210/pdb3ZK4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lupinus luteus
Mutation(s): No

Deposited: 2013-01-21 Released: 2014-01-29
Deposition Author(s): Antonyuk, S.V., Strange, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.175
R-Value Work: 0.150
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 199.88 kDa
Atom Count: 17,881
Modelled Residue Count: 1,708
Deposited Residue Count: 1,713
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPHOSPHONUCLEOTIDE PHOSPHATASE 1	A, B, C	571	Lupinus luteus	Mutation(s): 0 EC: 3.1.3.2
UniProt
Find proteins for Q8VX11 (Lupinus luteus) Explore Q8VX11 Go to UniProtKB: Q8VX11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VX11
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	D, E, F, G, H D, E, F, G, H, J	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain J Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, K	3		N-Glycosylation	Interactions Focus chain I Focus chain K Interactions & Density Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

Small Molecules

Ligands 5 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 C] SDF format, chain P [auth A] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain O [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	AA [auth C] BA [auth C] CA [auth C] O [auth A] P [auth A] AA [auth C], BA [auth C], CA [auth C], O [auth A], P [auth A], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain Q [auth A] SDF format, chain X [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth B]	DA [auth C], Q [auth A], X [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth C] Focus chain Q [auth A] Focus chain X [auth B] Interactions & Density Focus chain DA [auth C] Focus chain Q [auth A] Focus chain X [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth A] SDF format, chain EA [auth C] SDF format, chain R [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain R [auth A]	EA [auth C], N [auth A], R [auth A], S [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain N [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain EA [auth C] Focus chain N [auth A] Focus chain R [auth A] Focus chain S [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C]	L [auth A], T [auth B], Y [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain L [auth A] Focus chain T [auth B] Focus chain Y [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain Z [auth C] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C]	M [auth A], U [auth B], Z [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain M [auth A] Focus chain U [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.175
R-Value Work: 0.150
R-Value Observed: 0.151
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.925	α = 90
b = 223.925	β = 90
c = 111.904	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Antonyuk, S.V.

Strange, R.W.

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2014-03-12
Changes: Database references, Other, Structure summary
Version 1.2: 2014-08-20
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary