4B4X | pdb_00004b4x

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

PDB DOI: https://doi.org/10.2210/pdb4B4X/pdb

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

Deposited: 2012-08-01 Released: 2013-08-21
Deposition Author(s): Cannella, S.E., Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.268 (Depositor), 0.260 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a Complex between Actinomadura R39 Dd-Peptidase and a Boronate Inhibitor

Sauvage, E.

To be published.

Macromolecule Content

Total Structure Weight: 193.73 kDa
Atom Count: 13,905
Modeled Residue Count: 1,864
Deposited Residue Count: 1,864
Unique protein chains: 1

Macromolecules

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(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
HQZ Query on HQZ Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C]	BA [auth D], E [auth A], N [auth B], U [auth C]	trihydroxy{(1S)-1-[(methylsulfonyl)amino]ethyl}borate(1-) C₃ H₁₁ B N O₅ S ZTYRBLZCLIYDCR-GSVOUGTGSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain U [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] CA [auth D] DA [auth D] EA [auth D] F [auth A] AA [auth C], CA [auth D], DA [auth D], EA [auth D], F [auth A], FA [auth D], G [auth A], H [auth A], I [auth A], IA [auth D], JA [auth D], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	GA [auth D], HA [auth D], J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.268 (Depositor), 0.260 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.332	α = 90
b = 92.113	β = 95.9
c = 105.957	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary