4ZT5 - JenaLib

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Title :   TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR (2S)-N-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)-2-METHYLPROPANE-1,3-DIAMINE (CHEM 1655)

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 :   2.35

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, 14)

No.	Name	Count	Type	Full Name
1	4RN	1	Ligand/Ion	(2S)-N-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)-2-METHYLPROPANE-1,3-DIAMINE
2	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	6	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, 7)

No.	Name	Count	Type	Full Name
1	4RN	-1	Ligand/Ion	(2S)-N-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)-2-METHYLPROPANE-1,3-DIAMINE
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	4	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	4RN	1	Ligand/Ion	(2S)-N-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)-2-METHYLPROPANE-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:250 , ASP A:287 , TRP A:474 , ALA A:477 , TYR A:481 , ILE A:519 , HIS A:523 , LYS A:550 , HOH A:922	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	LYS A:521 , ILE A:525 , DMS A:804 , DMS A:806	binding site for residue DMS A 803
04	AC4	SOFTWARE	LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521 , DMS A:803	binding site for residue DMS A 804
05	AC5	SOFTWARE	TRP A:345 , GLU A:349 , PRO A:464	binding site for residue DMS A 805
06	AC6	SOFTWARE	LEU A:444 , DMS A:803	binding site for residue DMS A 806
07	AC7	SOFTWARE	ARG B:583 , ARG B:601 , HOH B:954	binding site for residue GOL B 801
08	AC8	SOFTWARE	GLU B:239 , ARG B:279 , LYS B:442 , GLY B:443 , PRO B:445 , GLU B:506	binding site for residue GOL B 802
09	AC9	SOFTWARE	PHE B:319 , TYR B:324 , ILE B:326 , HOH B:1072	binding site for residue DMS B 803
10	AD1	SOFTWARE	GLY B:573 , TYR B:574 , ASP B:575 , HOH B:948	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 , VAL B:471 , VAL B:473 , TRP B:474 , ASP B:476 , TYR B:481 , ILE B:519 , HOH B:918 , HOH B:922 , HOH B:931	binding site for residue 4RN B 806

(no "SS Bond" information available for 4ZT5)

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 4ZT5)

(no "PROSITE Motif" information available for 4ZT5)

(no "Exon" information available for 4ZT5)

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:522
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zt5 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTM 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  ||   566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766||
                                                                                                                                                                                                                                                                  470-CAS                                                                         550|                                                                                                                                                                                                            767|
                                                                                                                                                                                                                                                                                                                                                   560                                                                                                                                                                                                             801

Chain B from PDB  Type:PROTEIN  Length:528
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee...ee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee...ee..ee.........hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zt5 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371       389       399       409       419       429       439       449       459       469|      479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759        
                                0|                                                                                                                                           379|                                                                               470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                            388

Legend:		→ Mismatch	(orange background)
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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 4ZT5)

(no "CATH Domain" information available for 4ZT5)

(no "Pfam Domain" information available for 4ZT5)

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Asymmetric Unit
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	Cis Peptide Bonds
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		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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 14)

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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