4YCW | pdb_00004ycw

Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA synthetase mutant

PDB DOI: https://doi.org/10.2210/pdb4YCW/pdb

Classification: ligase/ligase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-02-20 Released: 2015-06-10
Deposition Author(s): Fang, P., Wang, J., Guo, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.268 (Depositor), 0.273 (DCC)
R-Value Work:
0.223 (Depositor), 0.227 (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 1.3 of the entry. See complete history.

Literature

Structural Basis for Specific Inhibition of tRNA Synthetase by ATP Competitive Inhibitor

Fang, P., Han, H., Wang, J., Chen, K., Chen, X., Guo, M.

(2015) Chem Biol 22: 1

Macromolecule Content

Total Structure Weight: 258.21 kDa
Atom Count: 16,000
Modeled Residue Count: 2,035
Deposited Residue Count: 2,220
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B, E, F	513	Homo sapiens	Mutation(s): 0 Gene Names: KARS, KIAA0070 EC: 6.1.1.6 (PDB Primary Data), 2.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15046 (Homo sapiens) Explore Q15046 Go to UniProtKB: Q15046
PHAROS: Q15046 GTEx: ENSG00000065427
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15046
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	C, D, G, H	42	Homo sapiens	Mutation(s): 0 Gene Names: AIMP2, JTV1, PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens) Explore Q13155 Go to UniProtKB: Q13155
PHAROS: Q13155 GTEx: ENSG00000106305
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13155
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
KRS	BindingDB: 4YCW	IC50: min: 2.00e+4, max: 1.05e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.268 (Depositor), 0.273 (DCC)
R-Value Work: 0.223 (Depositor), 0.227 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.283	α = 90.8
b = 75.561	β = 99.09
c = 162.987	γ = 109.83

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Fang, P.

Wang, J.

Guo, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM100136
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM106134

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description