2XK1

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

PDB DOI: https://doi.org/10.2210/pdb2XK1/pdb

Classification: HYDROLASE
Organism(s): Actinomadura sp. R39
Mutation(s): No

Deposited: 2010-07-07 Released: 2011-01-26
Deposition Author(s): Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.264
R-Value Work: 0.217
R-Value Observed: 0.219

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure Guided Development of Potent Reversibly Binding Penicillin Binding Protein Inhibitors

Woon, E.C.Y., Zervosen, A., Sauvage, E., Simmons, K.J., Ivec, M., Inglis, S.R., Fishwick, C.W.G., Gobec, S., Charlier, P., Luxen, A., Schofield, C.J.

(2011) ACS Med Chem Lett 2: 219

PubMed: 24900305 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ml100260x
Primary Citation of Related Structures:
2XK1, 2XLN

PubMed Abstract:
Following from the evaluation of different types of electrophiles, combined modeling and crystallographic analyses are used to generate potent boronic acid based inhibitors of a penicillin binding protein. The results suggest that a structurally informed approach to penicillin binding protein inhibition will be useful for the development of both improved reversibly binding inhibitors, including boronic acids, and acylating inhibitors, such as β-lactams.

Organizational Affiliation

Chemistry Research Laboratory, Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.

Macromolecule Content

Total Structure Weight: 193.56 kDa
Atom Count: 13,724
Modelled Residue Count: 1,862
Deposited Residue Count: 1,864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE	A, B, C, D	466	Actinomadura sp. R39	Mutation(s): 0 EC: 3.4.16.4
UniProt
Find proteins for P39045 (Actinomadura sp. (strain R39)) Explore P39045 Go to UniProtKB: P39045
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39045
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EWB Query on EWB Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	E [auth A], L [auth B], Q [auth C], V [auth D]	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) C₁₆ H₁₉ B N O₄ KXUAFLYMMJHXHZ-GFCCVEGCSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth B] F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	AA [auth D], BA [auth D], J [auth A], K [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
EWB	PDBBind: 2XK1	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.264
R-Value Work: 0.217
R-Value Observed: 0.219
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.898	α = 90
b = 92.348	β = 92.25
c = 143.829	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-26
Type: Initial release
Version 1.1: 2012-06-06
Changes: Database references, Version format compliance
Version 1.2: 2014-06-18
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary