1ROB

STRUCTURE OF THE CRYSTALLINE COMPLEX OF CYTIDYLIC ACID (2'-CMP) WITH RIBONUCLEASE AT 1.6 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1ROB/pdb

Classification: HYDROLASE(ENDORIBONUCLEASE)
Organism(s): Bos taurus
Mutation(s): No

Deposited: 1993-08-23 Released: 1994-01-31
Deposition Author(s): Lisgarten, J.N., Palmer, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 A resolution. Conservation of solvent sites in RNase-A high-resolution structures.

Lisgarten, J.N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R.A., Dealwis, C.G., Aguilar, C.F., Hemmings, A.M.

(1993) Acta Crystallogr D Biol Crystallogr 49: 541-547

PubMed: 15299491 Search on PubMed
DOI: https://doi.org/10.1107/S090744499300719X
Primary Citation of Related Structures:
1ROB

PubMed Abstract:
The X-ray structure of the inhibitor complex of bovine ribonuclease A with cytidylic acid (2'-CMP) has been determined at 1.6 A resolution and refined by restrained least squares to R = 0.17 for 11 945 reflections. Binding of the inhibitor molecule to the protein is confirmed to be in the productive mode associated with enzyme activity. A study of conserved solvent sites amongst high-resolution structures in the same crystal form reveals a stabilizing water cluster between the N and C termini.

Organizational Affiliation

Department of Ultrastructure, Institut voor Molekulaire Biologie, Vrije Universiteit Brussel, Sint Genesius Rode, Belgium.

Macromolecule Content

Total Structure Weight: 14.03 kDa
Atom Count: 1,077
Modelled Residue Count: 124
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE A	A	124	Bos taurus	Mutation(s): 0 EC: 3.1.27.5
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823 Go to UniProtKB: P61823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61823
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2P Query on C2P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CYTIDINE-2'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P YQUAKORMLHPSLZ-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
C2P	BindingDB: 1ROB	Ki: 7000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Observed: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.512	α = 90
b = 38.242	β = 106.1
c = 53.303	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1994-01-31

Deposition Author(s):

Lisgarten, J.N.

Revision History (Full details and data files)

Version 1.0: 1994-01-31
Type: Initial release
Version 1.1: 2008-03-24
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.