4MW5 - JenaLib

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Title :   TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA (CHEM 1415)

Authors :   C. Y. Koh, J. E. Kim, A. B. Wetzel, W. J. De Van Der Schueren, S. Shibata Z. Zhang, E. Fan, C. L. M. J. Verlinde, W. G. J. Hol

Date :   24 Sep 13 (Deposition) - 30 Apr 14 (Release) - 30 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Aminoacyl-Trna Synthetase, Aars, Metrs, Parasite, Protein-Inhibitor Complex, Rossmann Fold, Translation, Nucleotide Binding, Ligase- Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Y. Koh, J. E. Kim, A. B. Wetzel, W. J. De Van Der Schueren, S. Shibata, R. M. Ranade, J. Liu, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. Verlinde, E. Fan, W. G. Hol
Structures Of Trypanosoma Brucei Methionyl-Trna Synthetase With Urea-Based Inhibitors Provide Guidance For Drug Design Against Sleeping Sickness.
Plos Negl Trop Dis V. 8 E2775 2014
PubMed-ID: 24743796 | Reference-DOI: 10.1371/JOURNAL.PNTD.0002775

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
	Organism Taxid	:	5691

		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, 17)

No.	Name	Count	Type	Full Name
1	415	1	Ligand/Ion	1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	4	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	8	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	415	-1	Ligand/Ion	1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	2	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 2 (5, 10)

No.	Name	Count	Type	Full Name
1	415	1	Ligand/Ion	1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	5	Ligand/Ion	GLYCEROL
5	MET	-1	Mod. Amino Acid	METHIONINE
6	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:583 , ARG A:601	BINDING SITE FOR RESIDUE GOL A 901
02	AC2	SOFTWARE	ARG A:271 , VAL A:275 , SER A:714 , HOH A:1166	BINDING SITE FOR RESIDUE GOL A 902
03	AC3	SOFTWARE	GLU A:639 , GLN A:643 , LYS A:646 , HOH A:1058 , ARG B:358 , HIS B:654	BINDING SITE FOR RESIDUE GOL A 903
04	AC4	SOFTWARE	PHE A:370 , LYS A:521 , TYR A:526 , HOH A:1272	BINDING SITE FOR RESIDUE DMS A 904
05	AC5	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 , HOH A:1185 , HOH A:1186 , HOH A:1234	BINDING SITE FOR RESIDUE MET A 906
06	AC6	SOFTWARE	LYS B:347 , ARG B:486 , HOH B:1171	BINDING SITE FOR RESIDUE GOL B 901
07	AC7	SOFTWARE	ARG B:583 , ARG B:601	BINDING SITE FOR RESIDUE GOL B 902
08	AC8	SOFTWARE	HIS B:289 , THR B:333 , LYS B:338 , ASN B:458 , TRP B:459 , ALA B:460 , HOH B:1178	BINDING SITE FOR RESIDUE GOL B 903
09	AC9	SOFTWARE	ARG B:271 , VAL B:275 , PRO B:718 , SER B:721 , HOH B:1131 , HOH B:1247	BINDING SITE FOR RESIDUE GOL B 904
10	BC1	SOFTWARE	MET B:0 , GLU B:239 , TYR B:359 , PHE B:370 , MET B:406	BINDING SITE FOR RESIDUE GOL B 905
11	BC2	SOFTWARE	GLU B:320 , TYR B:324 , SER B:325 , ILE B:326 , HOH B:1053	BINDING SITE FOR RESIDUE DMS B 906
12	BC3	SOFTWARE	TYR B:472 , HOH B:1028	BINDING SITE FOR RESIDUE DMS B 907
13	BC4	SOFTWARE	ARG B:408 , ARG B:415 , HOH B:1186 , HOH B:1210	BINDING SITE FOR RESIDUE SO4 B 908
14	BC5	SOFTWARE	ILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , VAL B:471 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , LEU B:478 , ILE B:519 , PHE B:522 , HOH B:1014 , HOH B:1015	BINDING SITE FOR RESIDUE 415 B 909

(no "SS Bond" information available for 4MW5)

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 4MW5)

(no "PROSITE Motif" information available for 4MW5)

(no "Exon" information available for 4MW5)

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:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...............hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mw5 A 239 EKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKILGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468 |     478       488       498       508       518       528       538       548      |561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       
                                                                                                                                                                                                                                                                 470-CAS                                                                              555|                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                       559

Chain B from PDB  Type:PROTEIN  Length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee.....ee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee......hhhhh..hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mw5 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371       381|      397       407       417       427       437       447       457       467  |    477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767
                                0|                                                                                                                                             381|                                                                               470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                              388

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4MW5, only for superseded entry 3U1G replaced by 4MW5)

(no "CATH Domain" information available for 4MW5)

(no "Pfam Domain" information available for 4MW5)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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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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		Biological Unit 2	[ Jena3D ]

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4eg1	METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH SUBSTRATE METHIONINE
4eg3	METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INTERMEDIATE PRODUCT METHIONYL-ADENYLATE
4eg5	METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR CHEM 1312
4mvw
4mvx
4mvy
4mw0
4mw1
4mw2
4mw4
4mw6
4mw7
4mw9
4mwb
4mwc
4mwd
4mwe

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 17)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0 ; only for superseded entry 3U1G: 2,2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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