6HWR

Red kidney bean purple acid phosphatase in complex with adenosine divanadate

PDB DOI: https://doi.org/10.2210/pdb6HWR/pdb
Entry: 6HWR supersedes: 4KKZ

Classification: METAL BINDING PROTEIN
Organism(s): Phaseolus vulgaris
Mutation(s): No

Deposited: 2018-10-13 Released: 2019-04-03
Deposition Author(s): Feder, D., Gahan, L.R., McGeary, R.P., Guddat, L.W., Schenk, G.
Funding Organization(s): Australian Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.199
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Binding Mode of an ADP Analogue to a Metallohydrolase Mimics the Likely Transition State.

Feder, D., Gahan, L.R., McGeary, R.P., Guddat, L.W., Schenk, G.

(2019) Chembiochem 20: 1536-1540

PubMed: 30719821 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201900077
Primary Citation of Related Structures:
6HWR

PubMed Abstract:
Purple acid phosphatases (PAPs) are members of the large family of metallohydrolases, a group of enzymes that perform a wide range of biological functions, while employing a highly conserved catalytic mechanism. PAPs are found in plants, animals and fungi; in humans they play an important role in bone turnover and are thus of interest for developing treatments for osteoporosis. The majority of metallohydrolases use a metal-bound hydroxide to initiate catalysis, which leads to the formation of a proposed five-coordinate oxyphosphorane species in the transition state. In this work, we crystallized PAP from red kidney beans (rkbPAP) in the presence of both adenosine and vanadate. The in crystallo-formed vanadate analogue of ADP provides detailed insight into the binding mode of a PAP substrate, captured in a structure that mimics the putative fivecoordinate transition state. Our observations not only provide unprecedented insight into the mechanism of metallohydrolases, but might also guide the structure-based design of inhibitors for application in the treatment of several human illnesses.

Organizational Affiliation

School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.

Macromolecule Content

Total Structure Weight: 210.46 kDa
Atom Count: 17,001
Modelled Residue Count: 1,698
Deposited Residue Count: 1,704
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe(3+)-Zn(2+) purple acid phosphatase	A [auth C], B, C [auth A]	426	Phaseolus vulgaris	Mutation(s): 0 EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris) Explore P80366 Go to UniProtKB: P80366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80366
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A [auth C] Focus chain B Focus chain C [auth A]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe(3+)-Zn(2+) purple acid phosphatase	D	426	Phaseolus vulgaris	Mutation(s): 0 EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris) Explore P80366 Go to UniProtKB: P80366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80366
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	E, F, H	3		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain H
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H1T Query on H1T Download Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C]	Y [auth C]	[[[[bis($l^{1}-oxidanyl)-[$l^{1}-oxidanyl-[tris($l^{1}-oxidanyl)vanadiooxy]vanadio]oxy-vanadio]oxy-bis($l^{1}-oxidanyl)vanadio]oxy-oxidanylidene-vanadio]-[bis($l^{1}-oxidanyl)vanadio]-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)vanadium O₂₀ V₇ MFPKOXVPJRIEPC-UHFFFAOYSA-A		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
VV6 Query on VV6 Download Ideal Coordinates CCD File SDF format, chain QA [auth B] MOL2 format, chain QA [auth B]	QA [auth B]	[[[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxy-bis(oxidanyl)vanadio]-oxidanylidene-vanadio]oxy-oxidanyl-vanadio]oxy-tetrakis(oxidanyl)vanadium H₁₂ O₁₇ V₆ JXGHONBPQWTYGF-UHFFFAOYSA-B		Interactions Focus chain QA [auth B] Interactions & Density Focus chain QA [auth B]
H1Q Query on H1Q Download Ideal Coordinates CCD File SDF format, chain PB [auth A] MOL2 format, chain PB [auth A]	PB [auth A]	adenosine divanadate C₁₀ H₁₃ N₅ O₁₁ V₂ SCTBHSLYHREHHB-OUJHSJFHSA-M		Interactions Focus chain PB [auth A] Interactions & Density Focus chain PB [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain LB [auth A] SDF format, chain MB [auth A] SDF format, chain NA [auth B] SDF format, chain NC [auth D] SDF format, chain OA [auth B] SDF format, chain OC [auth D] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain LB [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NC [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain OC [auth D] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C]	LB [auth A] MB [auth A] NA [auth B] NC [auth D] OA [auth B] LB [auth A], MB [auth A], NA [auth B], NC [auth D], OA [auth B], OC [auth D], V [auth C], W [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NA [auth B] Focus chain NC [auth D] Focus chain OA [auth B] Focus chain OC [auth D] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NA [auth B] Focus chain NC [auth D] Focus chain OA [auth B] Focus chain OC [auth D] Focus chain V [auth C] Focus chain W [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain LC [auth D] SDF format, chain MC [auth D] SDF format, chain U [auth C] MOL2 format, chain LC [auth D] MOL2 format, chain MC [auth D] MOL2 format, chain U [auth C]	LC [auth D], MC [auth D], U [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain LC [auth D] Focus chain MC [auth D] Focus chain U [auth C] Interactions & Density Focus chain LC [auth D] Focus chain MC [auth D] Focus chain U [auth C]
H1W Query on H1W Download Ideal Coordinates CCD File SDF format, chain QC [auth D] MOL2 format, chain QC [auth D]	QC [auth D]	pentakis(oxidanyl)vanadium H₅ O₅ V QKDGGEBMABOMMW-UHFFFAOYSA-I		Interactions Focus chain QC [auth D] Interactions & Density Focus chain QC [auth D]
VN3 Query on VN3 Download Ideal Coordinates CCD File SDF format, chain SC [auth D] MOL2 format, chain SC [auth D]	SC [auth D]	VANADATE ION O₃ V YTVPPYMZCLYRBX-UHFFFAOYSA-N		Interactions Focus chain SC [auth D] Interactions & Density Focus chain SC [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain WB [auth D] SDF format, chain AB [auth A] SDF format, chain AC [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth A] SDF format, chain BC [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth A] SDF format, chain CC [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth A] SDF format, chain DC [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth A] SDF format, chain EC [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth A] SDF format, chain FC [auth D] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain SB [auth D] SDF format, chain TA [auth A] SDF format, chain TB [auth D] SDF format, chain UA [auth A] SDF format, chain UB [auth D] SDF format, chain VA [auth A] SDF format, chain VB [auth D] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain XB [auth D] SDF format, chain YA [auth A] SDF format, chain YB [auth D] SDF format, chain ZA [auth A] SDF format, chain ZB [auth D] MOL2 format, chain O [auth C] MOL2 format, chain WB [auth D] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain BC [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth A] MOL2 format, chain CC [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth A] MOL2 format, chain DC [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth A] MOL2 format, chain EC [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth A] MOL2 format, chain FC [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth D] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth D] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth D]	AB [auth A] AC [auth D] BA [auth B] BB [auth A] BC [auth D] AB [auth A], AC [auth D], BA [auth B], BB [auth A], BC [auth D], CA [auth B], CB [auth A], CC [auth D], DA [auth B], DB [auth A], DC [auth D], EA [auth B], EB [auth A], EC [auth D], FA [auth B], FB [auth A], FC [auth D], GA [auth B], HA [auth B], IA [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], SB [auth D], TA [auth A], TB [auth D], UA [auth A], UB [auth D], VA [auth A], VB [auth D], WA [auth A], WB [auth D], XA [auth A], XB [auth D], YA [auth A], YB [auth D], ZA [auth A], ZB [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth A] Focus chain AC [auth D] Focus chain BA [auth B] Focus chain BB [auth A] Focus chain BC [auth D] Focus chain CA [auth B] Focus chain CB [auth A] Focus chain CC [auth D] Focus chain DA [auth B] Focus chain DB [auth A] Focus chain DC [auth D] Focus chain EA [auth B] Focus chain EB [auth A] Focus chain EC [auth D] Focus chain FA [auth B] Focus chain FB [auth A] Focus chain FC [auth D] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain SB [auth D] Focus chain TA [auth A] Focus chain TB [auth D] Focus chain UA [auth A] Focus chain UB [auth D] Focus chain VA [auth A] Focus chain VB [auth D] Focus chain WA [auth A] Focus chain WB [auth D] Focus chain XA [auth A] Focus chain XB [auth D] Focus chain YA [auth A] Focus chain YB [auth D] Focus chain ZA [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth D] Focus chain BA [auth B] Focus chain BB [auth A] Focus chain BC [auth D] Focus chain CA [auth B] Focus chain CB [auth A] Focus chain CC [auth D] Focus chain DA [auth B] Focus chain DB [auth A] Focus chain DC [auth D] Focus chain EA [auth B] Focus chain EB [auth A] Focus chain EC [auth D] Focus chain FA [auth B] Focus chain FB [auth A] Focus chain FC [auth D] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain SB [auth D] Focus chain TA [auth A] Focus chain TB [auth D] Focus chain UA [auth A] Focus chain UB [auth D] Focus chain VA [auth A] Focus chain VB [auth D] Focus chain WA [auth A] Focus chain WB [auth D] Focus chain XA [auth A] Focus chain XB [auth D] Focus chain YA [auth A] Focus chain YB [auth D] Focus chain ZA [auth A] Focus chain ZB [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GB [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain R [auth C] MOL2 format, chain GB [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain R [auth C]	GB [auth A], JA [auth B], KA [auth B], LA [auth B], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GB [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain R [auth C] Interactions & Density Focus chain GB [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain R [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain QB [auth D] SDF format, chain RA [auth A] SDF format, chain Z [auth B] MOL2 format, chain I [auth C] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth A] MOL2 format, chain Z [auth B]	I [auth C], QB [auth D], RA [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain QB [auth D] Focus chain RA [auth A] Focus chain Z [auth B] Interactions & Density Focus chain I [auth C] Focus chain QB [auth D] Focus chain RA [auth A] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GC [auth D] SDF format, chain HB [auth A] SDF format, chain HC [auth D] SDF format, chain IB [auth A] SDF format, chain IC [auth D] SDF format, chain JB [auth A] SDF format, chain JC [auth D] SDF format, chain KB [auth A] SDF format, chain KC [auth D] SDF format, chain MA [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain GC [auth D] MOL2 format, chain HB [auth A] MOL2 format, chain HC [auth D] MOL2 format, chain IB [auth A] MOL2 format, chain IC [auth D] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth D] MOL2 format, chain KB [auth A] MOL2 format, chain KC [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	GC [auth D] HB [auth A] HC [auth D] IB [auth A] IC [auth D] GC [auth D], HB [auth A], HC [auth D], IB [auth A], IC [auth D], JB [auth A], JC [auth D], KB [auth A], KC [auth D], MA [auth B], S [auth C], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GC [auth D] Focus chain HB [auth A] Focus chain HC [auth D] Focus chain IB [auth A] Focus chain IC [auth D] Focus chain JB [auth A] Focus chain JC [auth D] Focus chain KB [auth A] Focus chain KC [auth D] Focus chain MA [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain GC [auth D] Focus chain HB [auth A] Focus chain HC [auth D] Focus chain IB [auth A] Focus chain IC [auth D] Focus chain JB [auth A] Focus chain JC [auth D] Focus chain KB [auth A] Focus chain KC [auth D] Focus chain MA [auth B] Focus chain S [auth C] Focus chain T [auth C]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain RC [auth D] MOL2 format, chain RC [auth D]	RC [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain RC [auth D] Interactions & Density Focus chain RC [auth D]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain RB [auth D] SDF format, chain AA [auth B] SDF format, chain J [auth C] SDF format, chain SA [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain J [auth C] MOL2 format, chain SA [auth A]	AA [auth B], J [auth C], RB [auth D], SA [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain J [auth C] Focus chain RB [auth D] Focus chain SA [auth A] Interactions & Density Focus chain AA [auth B] Focus chain J [auth C] Focus chain RB [auth D] Focus chain SA [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain NB [auth A] SDF format, chain OB [auth A] SDF format, chain PA [auth B] SDF format, chain PC [auth D] SDF format, chain X [auth C] MOL2 format, chain NB [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PC [auth D] MOL2 format, chain X [auth C]	NB [auth A], OB [auth A], PA [auth B], PC [auth D], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PA [auth B] Focus chain PC [auth D] Focus chain X [auth C] Interactions & Density Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PA [auth B] Focus chain PC [auth D] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.199
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.242	α = 90
b = 126.242	β = 90
c = 296.877	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-03

Deposition Author(s):

This entry supersedes: 4KKZ

Funding Organization	Location	Grant Number
Australian Research Council	Australia	DP150104358

Revision History (Full details and data files)

Version 1.0: 2019-04-03
Type: Initial release
Version 1.1: 2019-04-10
Changes: Data collection, Database references
Version 1.2: 2019-06-26
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary