6AQH | pdb_00006aqh

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium thermoresistibile complexed with L-lysine and Cladosporin

PDB DOI: https://doi.org/10.2210/pdb6AQH/pdb

Classification: LIGASE/INHIBITOR
Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-19 Released: 2017-08-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.254 (Depositor), 0.260 (DCC)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium thermoresistibile complexed with L-lysine and Cladosporin

Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 229.84 kDa
Atom Count: 15,398
Modeled Residue Count: 1,953
Deposited Residue Count: 2,032
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B, C, D	508	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0 Gene Names: lysS, KEK_07907 EC: 6.1.1.6
UniProt
Find proteins for G7CF12 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CF12 Go to UniProtKB: G7CF12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G7CF12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KRS Query on KRS Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], L [auth C], N [auth D]	cladosporin C₁₆ H₂₀ O₅ WOMKDMUZNBFXKG-ZWKOPEQDSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D]
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B]	E [auth A], G [auth B], K [auth C], M [auth D]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]