4A6A

A115V variant of dCTP deaminase-dUTPase from Mycobacterium tuberculosis in complex with dTTP

PDB DOI: https://doi.org/10.2210/pdb4A6A/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-11-01 Released: 2012-10-10
Deposition Author(s): Lovgreen, M.N., Ucar, E., Willemoes, M., Harris, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.290
R-Value Work: 0.253
R-Value Observed: 0.255

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Dttp Inhibition of the Bifunctional Dctp Deaminase- Dutpase from Mycobacterium Tuberculosis is Ph Dependent: Kinetic Analyses and Crystal Structure of A115V Variant

Lovgreen, M.N., Harris, P., Ucar, E., Willemoes, M.

To be published.

Macromolecule Content

Total Structure Weight: 257.16 kDa
Atom Count: 17,912
Modelled Residue Count: 2,263
Deposited Residue Count: 2,280
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	190	Mycobacterium tuberculosis H37Rv	Mutation(s): 1 EC: 3.5.4.13 (PDB Primary Data), 3.5.4.30 (UniProt)
UniProt
Find proteins for P9WP17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP17 Go to UniProtKB: P9WP17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WP17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TTP Query on TTP Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain EA [auth I] SDF format, chain GA [auth J] SDF format, chain IA [auth K] SDF format, chain KA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain KA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain KA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G]	BA [auth H] EA [auth I] GA [auth J] IA [auth K] KA [auth L] BA [auth H], EA [auth I], GA [auth J], IA [auth K], KA [auth L], M [auth A], O [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	THYMIDINE-5'-TRIPHOSPHATE C₁₀ H₁₇ N₂ O₁₄ P₃ NHVNXKFIZYSCEB-XLPZGREQSA-N		Interactions Focus chain BA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth H] SDF format, chain DA [auth H] SDF format, chain FA [auth I] SDF format, chain HA [auth J] SDF format, chain JA [auth K] SDF format, chain LA [auth L] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain LA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain FA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain JA [auth K] mmCIF format, chain LA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F]	AA [auth G] CA [auth H] DA [auth H] FA [auth I] HA [auth J] AA [auth G], CA [auth H], DA [auth H], FA [auth I], HA [auth J], JA [auth K], LA [auth L], N [auth A], P [auth B], Q [auth B], S [auth C], U [auth D], W [auth E], Y [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.290
R-Value Work: 0.253
R-Value Observed: 0.255
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.59	α = 90
b = 179.51	β = 96.28
c = 99.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-12-26
Changes: Structure summary
Version 1.2: 2017-11-08
Changes: Source and taxonomy
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description