4QTF

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

PDB DOI: https://doi.org/10.2210/pdb4QTF/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-07 Released: 2015-07-29
Deposition Author(s): Gokulan, K., Varughese, K.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Khare, S., Cerniglia, C.E., Foley, S.L., Varughese, K.I.

To be published.

Macromolecule Content

Total Structure Weight: 38.59 kDa
Atom Count: 2,776
Modelled Residue Count: 349
Deposited Residue Count: 349
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,d-transpeptidase LdtB	A	349	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ldtB, Rv2518c, RVBD_2518c
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6Y9J2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLD Query on MLD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA C₃₇ H₅₉ N₇ O₂₀ UPFMKPIBAIPLHT-RSJSDIDPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
3V5 Query on 3V5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(3S,5S)-3-({[(aminomethyl)amino]methyl}sulfanyl)-5-[(2S)-1,3-dioxobutan-2-yl]-L-proline C₁₁ H₁₉ N₃ O₄ S SKDDBJCIWUNJNL-XKNYDFJKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.272	α = 90
b = 65.881	β = 90
c = 207.456	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Gokulan, K.

Varughese, K.I.

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2016-08-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4QTF

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

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)