1UCD | pdb_00001ucd

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.203 (Depositor) 
• R-Value Work: 
  0.200 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	B [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
URA	C [auth A]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.203 (Depositor) 
• R-Value Work:  0.200 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Suzuki, A., Numata, T., Yao, M., Kimura, M., Tanaka, I.

Revision History  

• 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
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary