3S8B

Structure of Yeast Ribonucleotide Reductase 1 with AMPPNP and CDP

PDB DOI: https://doi.org/10.2210/pdb3S8B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-27 Released: 2012-04-11
Deposition Author(s): Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.250
R-Value Work: 0.209
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase

Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 100.61 kDa
Atom Count: 5,322
Modelled Residue Count: 659
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase large chain 1	A	888	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CRT7, RIR1, RNR1, Saccharomyces, SDS12, YER070W EC: 1.17.4.1
UniProt
Find proteins for P21524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21524 Go to UniProtKB: P21524
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21524
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CDP Query on CDP 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]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.250
R-Value Work: 0.209
R-Value Observed: 0.213
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.869	α = 90
b = 117.567	β = 90
c = 64.967	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-11
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 1.2: 2024-02-28
Changes: Advisory, Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

3S8B

Structure of Yeast Ribonucleotide Reductase 1 with AMPPNP and CDP

Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)