6LQB

A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct

PDB DOI: https://doi.org/10.2210/pdb6LQB/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-13 Released: 2021-01-13
Deposition Author(s): Li, D.F., Qin, Y.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A New State I-plus Observed for the L,D-transpeptidase LdtMt2-ertapenem Adduct

Wang, X.Y., Qin, Y.L., Han, Q., Gu, X.E., Yan, Z., Fu, K., Li, D.F., Deng, K.

(2020) PROG BIOCHEM BIOPHYS 47: 989-997

DOI: https://doi.org/10.16476/j.pibb.2020.0079

Macromolecule Content

Total Structure Weight: 59.94 kDa
Atom Count: 4,578
Modelled Residue Count: 531
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A, B	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6Y9J2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2RG (Subject of Investigation/LOI) Query on 2RG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C₂₂ H₂₇ N₃ O₇ S RALHTEQYPKBGFO-SAGZMZRGSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	D [auth A], E [auth A], F [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.181	α = 90
b = 73.207	β = 90
c = 103.803	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-01-13

Deposition Author(s):

Li, D.F.

Qin, Y.L.

Revision History (Full details and data files)

Version 1.0: 2021-01-13
Type: Initial release
Version 1.1: 2021-07-28
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary

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Help and Resources

6LQB

A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct

A New State I-plus Observed for the L,D-transpeptidase LdtMt2-ertapenem Adduct

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)