4KBP

KIDNEY BEAN PURPLE ACID PHOSPHATASE

PDB DOI: https://doi.org/10.2210/pdb4KBP/pdb

Classification: HYDROLASE (PHOSPHORIC MONOESTER)
Organism(s): Phaseolus vulgaris
Mutation(s): No

Deposited: 1995-10-02 Released: 1996-12-07
Deposition Author(s): Klabunde, T., Strater, N., Krebs, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.228
R-Value Work: 0.192
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 206.51 kDa
Atom Count: 14,340
Modelled Residue Count: 1,696
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PURPLE ACID PHOSPHATASE	A, B, C, D	432	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain E [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain E [auth A]	CA [auth D] DA [auth D] E [auth A] EA [auth D] F [auth A] CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B]	BA [auth C], JA [auth D], L [auth A], T [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain T [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain IA [auth D] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	AA [auth C], IA [auth D], K [auth A], S [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain S [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C]	HA [auth D], J [auth A], R [auth B], Z [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.228
R-Value Work: 0.192
R-Value Observed: 0.192
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.7	α = 90
b = 347.3	β = 90
c = 128.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1996-12-07

Deposition Author(s):

Klabunde, T.

Strater, N.

Krebs, B.

Revision History (Full details and data files)

Version 1.0: 1996-12-07
Type: Initial release
Version 1.1: 2008-03-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary