8JCQ

Crystal structure of Procerain from Calotropis gigantea

PDB DOI: https://doi.org/10.2210/pdb8JCQ/pdb

Classification: HYDROLASE
Organism(s): Calotropis gigantea
Mutation(s): No

Deposited: 2023-05-11 Released: 2024-05-22
Deposition Author(s): Kumar, A., Jamdar, S.N., Srivastava, G., Makde, R.D.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.182
R-Value Work: 0.164
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Procerain from Calotropis gigantea

Kumar, A., Jamdar, S.N., Srivastava, G., Makde, R.D.

To be published.

Macromolecule Content

Total Structure Weight: 23.75 kDa
Atom Count: 2,010
Modelled Residue Count: 214
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procerain	A	214	Calotropis gigantea	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E64 (Subject of Investigation/LOI) Query on E64 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C₁₅ H₃₀ N₅ O₅ QPQNJAXBPHVASB-QWRGUYRKSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.182
R-Value Work: 0.164
R-Value Observed: 0.165
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.616	α = 90
b = 121.272	β = 90
c = 61.006	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
RESOLVE	model building
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.