4EBP | pdb_00004ebp

BlaC E166A Cefotaxime Acyl-Intermediate Complex

PDB DOI: https://doi.org/10.2210/pdb4EBP/pdb

Classification: Hydrolase/Antibiotic
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-03-23 Released: 2013-04-03
Deposition Author(s): Mire, J.A., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Faropenem is Effective Against Mycobacterium tuberculosis in vitro and in vivo

Mire, J.A., Pai, P., Siddiqi, N., Russell, D.H., Rubin, E.J., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 114.51 kDa
Atom Count: 7,948
Modeled Residue Count: 1,046
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	265	Mycobacterium tuberculosis	Mutation(s): 1 Gene Names: blaA, blaC, MT2128, MTCY49.07c, Rv2068c EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD3 Go to UniProtKB: P9WKD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CEF Query on CEF Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	I [auth B], K [auth C]	CEFOTAXIME, C3' cleaved, open, bound form C₁₄ H₁₅ N₅ O₅ S₂ NRYMPLKBKFIWQC-YVCCLBOHSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain I [auth B] Focus chain K [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], L [auth C], M [auth D], N [auth D], O [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.240 (Depositor), 0.241 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.82	α = 90
b = 96.152	β = 106.34
c = 107.088	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Mire, J.A.

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 2.0: 2018-09-19
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.2: 2024-11-20
Changes: Structure summary

4EBP | pdb_00004ebp

BlaC E166A Cefotaxime Acyl-Intermediate Complex

Literature

Faropenem is Effective Against Mycobacterium tuberculosis in vitro and in vivo

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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