Macromolecule Content

Total Structure Weight: 21.66 kDa
Atom Count: 1,764
Modelled Residue Count: 190
Deposited Residue Count: 190
Unique protein chains: 1

1UCD

Crystal structure of Ribonuclease MC1 from bitter gourd seeds complexed with 5'-UMP

PDB DOI: https://doi.org/10.2210/pdb1UCD/pdb

Classification: HYDROLASE
Organism(s): Momordica charantia
Mutation(s): No

Deposited: 2003-04-10 Released: 2004-05-18
Deposition Author(s): Suzuki, A., Numata, T., Yao, M., Kimura, M., Tanaka, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.203
R-Value Work: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of RNase MC1 from bitter gourd seeds in complex with 5'UMP

Suzuki, A., Numata, T., Yao, M., Kimura, M., Tanaka, I.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease MC	A	190	Momordica charantia	Mutation(s): 0 EC: 3.1.27.1 (PDB Primary Data), 4.6.1.19 (UniProt)
UniProt
Find proteins for P23540 (Momordica charantia) Explore P23540 Go to UniProtKB: P23540
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23540
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Ligand Interaction
URA Query on URA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.203
R-Value Work: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.18	α = 90
b = 63.48	β = 90
c = 73.74	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-05-18
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.