1RNT

RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF THE RIBONUCLEASE T1(ASTERISK)2(PRIME)-GUANYLIC ACID COMPLEX AT 1.9 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1RNT/pdb

Classification: HYDROLASE(ENDORIBONUCLEASE)
Organism(s): Aspergillus oryzae
Mutation(s): No

Deposited: 1987-07-10 Released: 1987-10-16
Deposition Author(s): Saenger, W., Arni, R., Heinemann, U., Tokuoka, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1(Asterisk)2(Prime)-Guanylic Acid Complex at 1.9 Angstroms Resolution

Arni, R., Heinemann, U., Maslowska, M., Tokuoka, R., Saenger, W.

(1987) Acta Crystallogr B 43: 548

Macromolecule Content

Total Structure Weight: 11.46 kDa
Atom Count: 892
Modelled Residue Count: 104
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE T1 ISOZYME	A	104	Aspergillus oryzae	Mutation(s): 0 EC: 3.1.27.3
UniProt
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P00651 Go to UniProtKB: P00651
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2GP Query on 2GP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GUANOSINE-2'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P WTIFIAZWCCBCGE-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
2GP	PDBBind: 1RNT	Kd: 6500 (nM) from 1 assay(s)
2GP	Binding MOAD: 1RNT	Kd: 6500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.81	α = 90
b = 50.11	β = 90
c = 40.44	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1987-10-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1987-10-16
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-11-29
Changes: Derived calculations, Other

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.