6I1F

Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with amoxicillin

PDB DOI: https://doi.org/10.2210/pdb6I1F/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Chlamydia trachomatis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-28 Released: 2019-11-20
Deposition Author(s): Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.246
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with amoxicillin

Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 73.67 kDa
Atom Count: 5,266
Modelled Residue Count: 685
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein,Penicillin-binding protein	A, B	346	Chlamydia trachomatis	Mutation(s): 0 Gene Names: pbp_2, ERS133248_00492 EC: 2.4.1.129
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AXL (Subject of Investigation/LOI) Query on AXL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID C₁₆ H₂₁ N₃ O₅ S SMLJDSWXGVMNTH-NRWUCQMLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.246
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.226	α = 90
b = 106.226	β = 90
c = 118.554	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	grant.MR/P007503/1

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.