4ZT3 - JenaLib

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Title :   TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR N-(3,5-DICHLOROBENZYL)-N'-(5-FLUORO-1H-IMIDAZO[4,5-B]PYRIDIN-2-YL) PROPANE-1,3-DIAMINE (CHEM 1614)

Authors :   C. -Y. Koh, W. G. J. Hol

Date :   14 May 15 (Deposition) - 04 May 16 (Release) - 12 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ligase, Aminoacyl-Trna Synthetase, Aars, Metrs, Trypanosoma Brucei, Protein-Inhibitor Complex, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, C. Y. Koh, R. M. Ranade, S. Shibata, J. R. Gillespie, M. A. Hulverson, W. Huang, J. Nguyen, N. Pendem, M. H. Gelb, C. L. Verlinde, W. G. Hol, F. S. Buckner, E. Fan
5-Fluoroimidazo[4, 5-B]Pyridine Is A Privileged Fragment Tha Conveys Bioavailability To Potent Trypanosomal Methionyl-Trna Synthetase Inhibitors.
Acs Infect Dis. V. 2 399 2016
PubMed-ID: 27627628 | Reference-DOI: 10.1021/ACSINFECDIS.6B00036

Molecule 1 - METHIONYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 237-773
	Gene	:	TB10.70.6470
	Mutation	:	YES
	Organism Scientific	:	TRYPANOSOMA BRUCEI BRUCEI
	Organism Taxid	:	185431
	Strain	:	927/4 GUTAT10.1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 15)

No.	Name	Count	Type	Full Name
1	4RQ	1	Ligand/Ion	N-(3,5-DICHLOROBENZYL)-N'-(5-FLUORO-1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	7	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	3	Ligand/Ion	GLYCEROL
5	MET	1	Mod. Amino Acid	METHIONINE
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	4RQ	-1	Ligand/Ion	N-(3,5-DICHLOROBENZYL)-N'-(5-FLUORO-1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	5	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	1	Ligand/Ion	GLYCEROL
5	MET	1	Mod. Amino Acid	METHIONINE
6	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (5, 7)

No.	Name	Count	Type	Full Name
1	4RQ	1	Ligand/Ion	N-(3,5-DICHLOROBENZYL)-N'-(5-FLUORO-1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	2	Ligand/Ion	GLYCEROL
5	MET	-1	Mod. Amino Acid	METHIONINE
6	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:248 , TYR A:249 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , TYR A:481 , HIS A:523 , LYS A:550 , HOH A:946	binding site for residue MET A 801
02	AC2	SOFTWARE	ARG A:583 , ARG A:601	binding site for residue GOL A 802
03	AC3	SOFTWARE	GLU A:392 , LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521	binding site for residue DMS A 804
04	AC4	SOFTWARE	PHE A:370 , PRO A:445 , LYS A:521 , TYR A:526	binding site for residue DMS A 805
05	AC5	SOFTWARE	GLU A:349 , TYR A:405 , VAL A:463 , PRO A:464	binding site for residue DMS A 806
06	AC6	SOFTWARE	ARG A:271 , SER A:714 , PRO A:718	binding site for residue DMS A 807
07	AC7	SOFTWARE	ARG B:583 , ARG B:601	binding site for residue GOL B 801
08	AC8	SOFTWARE	TYR B:472 , TRP B:474 , PHE B:522 , 4RQ B:806 , HOH B:926 , HOH B:982	binding site for residue GOL B 802
09	AC9	SOFTWARE	TYR B:324 , ILE B:326 , HOH B:914 , HOH B:953	binding site for residue DMS B 803
10	AD1	SOFTWARE	TYR B:574 , ARG B:719 , LYS B:720 , HOH B:986	binding site for residue DMS B 804
11	AD2	SOFTWARE	ARG B:271 , VAL B:275 , SER B:714 , PRO B:718	binding site for residue SO4 B 805
12	AD3	SOFTWARE	ILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , LEU B:456 , TYR B:472 , VAL B:473 , TYR B:481 , ILE B:519 , PHE B:522 , GOL B:802 , HOH B:922 , HOH B:960 , HOH B:998	binding site for residue 4RQ B 806

(no "SS Bond" information available for 4ZT3)

Asymmetric Unit

No.	Residues
1	Val A:428	-	Pro A:429
2	Phe A:508	-	Pro A:509
3	Ile A:658	-	Pro A:659
4	Val B:428	-	Pro B:429
5	Phe B:508	-	Pro B:509
6	Ile B:658	-	Pro B:659

(no "SAP(SNP)/Variant" information available for 4ZT3)

(no "PROSITE Motif" information available for 4ZT3)

(no "Exon" information available for 4ZT3)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee.........ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zt3 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEVLFSKRSTM 801
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  |    477       487       497       507       517       527       537       547  ||   567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       759       ||
                                                                                                                                                                                                                                                                  470-CAS                                                                         550|                                                                                                                                                                                                756|     767|
                                                                                                                                                                                                                                                                                                                                                   561                                                                                                                                                                                                 759      801

Chain B from PDB  Type:PROTEIN  Length:526
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhhhh..........eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee.........ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh......eeee..eee.............hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zt3 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371     ||391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761      
                                0|                                                                                                                                         377|                                                                               470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                          388

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4ZT3)

(no "CATH Domain" information available for 4ZT3)

(no "Pfam Domain" information available for 4ZT3)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:658 - Pro A:659	[ RasMol ]
		Ile B:658 - Pro B:659	[ RasMol ]
		Phe A:508 - Pro A:509	[ RasMol ]
		Phe B:508 - Pro B:509	[ RasMol ]
		Val A:428 - Pro A:429	[ RasMol ]
		Val B:428 - Pro B:429	[ RasMol ]

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	4zt3
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (10, 10)

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