3VFH

BlaC E166A CDC-1 Acyl-Intermediate

PDB DOI: https://doi.org/10.2210/pdb3VFH/pdb

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

Deposited: 2012-01-09 Released: 2012-09-19
Deposition Author(s): Mire, J.A., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.252
R-Value Work: 0.225
R-Value Observed: 0.227

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

BlaC-Specific Fluorogenic Probes for Rapid Tuberculosis Detection

Xie, H., Mire, J.A., Kong, Y., Chang, M., Sacchettini, J.C., Cirillo, J.D., Rao, J.

To be published.

Macromolecule Content

Total Structure Weight: 123.29 kDa
Atom Count: 8,123
Modelled Residue Count: 1,060
Deposited Residue Count: 1,140
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	285	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WKD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD6 Query on CD6 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	H [auth B], J [auth C]	(2R)-5-methylidene-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid C₁₆ H₁₆ N₂ O₄ S ISCTZDPSWLBTMN-IUODEOHRSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth B] Focus chain J [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	E [auth A] F [auth A] G [auth A] I [auth B] K [auth C] E [auth A], F [auth A], G [auth A], I [auth B], K [auth C], L [auth D], M [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 I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.252
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.396	α = 90
b = 97.459	β = 108.37
c = 110.958	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Mire, J.A.

Sacchettini, J.C.

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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Deposit Data

Help and Resources

3VFH

BlaC E166A CDC-1 Acyl-Intermediate

BlaC-Specific Fluorogenic Probes for Rapid Tuberculosis Detection

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)