6HWR

Red kidney bean purple acid phosphatase in complex with adenosine divanadate


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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Ligand Structure Quality Assessment 


This is version 2.2 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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fe(3+)-Zn(2+) purple acid phosphataseA [auth C],
B,
C [auth A]
426Phaseolus vulgarisMutation(s): 0 
EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris)
Explore P80366 
Go to UniProtKB:  P80366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80366
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fe(3+)-Zn(2+) purple acid phosphatase426Phaseolus vulgarisMutation(s): 0 
EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris)
Explore P80366 
Go to UniProtKB:  P80366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80366
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H1T
Query on H1T

Download Ideal Coordinates CCD File 
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
VV6
Query on VV6

Download Ideal Coordinates CCD File 
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
H1Q
Query on H1Q

Download Ideal Coordinates CCD File 
PB [auth A]adenosine divanadate
C10 H13 N5 O11 V2
SCTBHSLYHREHHB-OUJHSJFHSA-M
NAG
Query on NAG

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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
PGE
Query on PGE

Download Ideal Coordinates CCD File 
LC [auth D],
MC [auth D],
U [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
H1W
Query on H1W

Download Ideal Coordinates CCD File 
QC [auth D]pentakis(oxidanyl)vanadium
H5 O5 V
QKDGGEBMABOMMW-UHFFFAOYSA-I
VN3
Query on VN3

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SC [auth D]VANADATE ION
O3 V
YTVPPYMZCLYRBX-UHFFFAOYSA-N
SO4
Query on SO4

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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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GB [auth A],
JA [auth B],
KA [auth B],
LA [auth B],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth C],
QB [auth D],
RA [auth A],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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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
IPA
Query on IPA

Download Ideal Coordinates CCD File 
RC [auth D]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
FE
Query on FE

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AA [auth B],
J [auth C],
RB [auth D],
SA [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
NB [auth A],
OB [auth A],
PA [auth B],
PC [auth D],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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 = 126.242α = 90
b = 126.242β = 90
c = 296.877γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research CouncilAustraliaDP150104358

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
  • Version 2.2: 2024-10-23
    Changes: Structure summary