1VD3 | pdb_00001vd3

Ribonuclease NT in complex with 2'-UMP

PDB DOI: https://doi.org/10.2210/pdb1VD3/pdb

Classification: HYDROLASE
Organism(s): Nicotiana glutinosa
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2004-03-18 Released: 2005-04-26
Deposition Author(s): Kawano, S., Kakuta, Y., Kimura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.209 (Depositor), 0.208 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1VD3

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Nicotiana glutinosa Ribonuclease NT in Complex with Nucleotide Monophosphates

Kawano, S., Kakuta, Y., Kimura, M.

To be published.

Macromolecule Content

Total Structure Weight: 25.32 kDa
Atom Count: 1,764
Modeled Residue Count: 204
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNase NGR3	A	217	Nicotiana glutinosa	Mutation(s): 0 EC: 3.1.27.1
UniProt
Find proteins for Q9SSV1 (Nicotiana glutinosa) Explore Q9SSV1 Go to UniProtKB: Q9SSV1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SSV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U2P Query on U2P Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER C₉ H₁₃ N₂ O₉ P HQIDPEYTETUCNF-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.209 (Depositor), 0.208 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.232	α = 90
b = 68.984	β = 90
c = 73.863	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-04-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-26
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: 2024-10-30
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.