3TP1

Crystal Structure of the precatalytic M-PMV dUTPase - substrate (dUPNPP) complex

PDB DOI: https://doi.org/10.2210/pdb3TP1/pdb

Classification: HYDROLASE
Organism(s): Mason-Pfizer monkey virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-09-07 Released: 2011-09-21
Deposition Author(s): Barabas, O., Nemeth, V., Vertessy, B.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.197
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion

Barabas, O., Nemeth, V., Bodor, A., Perczel, A., Rosta, E., Kele, Z., Zagyva, I., Szabadka, Z., Grolmusz, V.I., Wilmanns, M., Vertessy, B.G.

To be published.

Macromolecule Content

Total Structure Weight: 16.66 kDa
Atom Count: 1,011
Modelled Residue Count: 114
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE	A	152	Mason-Pfizer monkey virus	Mutation(s): 1 Gene Names: gag-pro EC: 3.6.1.23
UniProt
Find proteins for P07570 (Mason-Pfizer monkey virus) Explore P07570 Go to UniProtKB: P07570
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DUP Query on DUP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ XZLLMTSKYYYJLH-SHYZEUOFSA-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 C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.197
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.596	α = 90
b = 60.596	β = 90
c = 63.862	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Barabas, O.

Nemeth, V.

Vertessy, B.G.

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection

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3TP1

Crystal Structure of the precatalytic M-PMV dUTPase - substrate (dUPNPP) complex

Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)