4MVY - JenaLib

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Title :   TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-(3-HYDROXYPHENYL)UREA (CHEM 1387)

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 :   2.31

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 (5, 15)

No.	Name	Count	Type	Full Name
1	387	1	Ligand/Ion	1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-(3-HYDROXYPHENYL)UREA
2	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	8	Ligand/Ion	GLYCEROL
5	MET	1	Mod. Amino Acid	METHIONINE

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	387	-1	Ligand/Ion	1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-(3-HYDROXYPHENYL)UREA
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	4	Ligand/Ion	GLYCEROL
5	MET	1	Mod. Amino Acid	METHIONINE

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	387	1	Ligand/Ion	1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-(3-HYDROXYPHENYL)UREA
2	CAS	1	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	4	Ligand/Ion	GLYCEROL
5	MET	-1	Mod. Amino Acid	METHIONINE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:345 , GLU A:349 , TYR A:405 , PRO A:464	BINDING SITE FOR RESIDUE GOL A 801
02	AC2	SOFTWARE	HIS A:289 , LYS A:338 , ASN A:458 , TRP A:459 , ALA A:460 , PRO A:462	BINDING SITE FOR RESIDUE GOL A 802
03	AC3	SOFTWARE	ARG A:719	BINDING SITE FOR RESIDUE GOL A 803
04	AC4	SOFTWARE	LYS A:521 , DMS A:805 , HOH A:1025 , HOH A:1106 , HOH A:1178	BINDING SITE FOR RESIDUE DMS A 804
05	AC5	SOFTWARE	DMS A:804	BINDING SITE FOR RESIDUE DMS A 805
06	AC6	SOFTWARE	ARG A:583 , ARG A:601	BINDING SITE FOR RESIDUE GOL A 806
07	AC7	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:978 , HOH A:979	BINDING SITE FOR RESIDUE MET A 807
08	AC8	SOFTWARE	GLU B:343 , LYS B:347 , LEU B:482 , ARG B:486 , HOH B:981	BINDING SITE FOR RESIDUE GOL B 801
09	AC9	SOFTWARE	ARG B:583 , ARG B:601	BINDING SITE FOR RESIDUE GOL B 802
10	BC1	SOFTWARE	HIS B:289 , THR B:333 , LYS B:338 , ASN B:458 , TRP B:459 , ALA B:460 , CAS B:470	BINDING SITE FOR RESIDUE GOL B 803
11	BC2	SOFTWARE	ASN B:612 , ARG B:616 , HOH B:935	BINDING SITE FOR RESIDUE GOL B 804
12	BC3	SOFTWARE	GLU B:320 , TYR B:324 , SER B:325 , ILE B:326 , HOH B:1106	BINDING SITE FOR RESIDUE DMS B 805
13	BC4	SOFTWARE	ILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , LEU B:456 , VAL B:471 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , ALA B:477 , TYR B:481 , ILE B:519 , HIS B:523 , HOH B:995 , HOH B:1080 , HOH B:1128 , HOH B:1167	BINDING SITE FOR RESIDUE 387 B 806

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

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 4MVY)

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

(no "Exon" information available for 4MVY)

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:531
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvy A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                   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       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 
                                                                                                                                                                                                                                                                  470-CAS

Chain B from PDB  Type:PROTEIN  Length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee.....ee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee...ee.............hhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhh.hhhhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvy 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)
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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 4MVY, only for superseded entry 3U1E replaced by 4MVY)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		387	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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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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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
4mw0
4mw1
4mw2
4mw4
4mw5
4mw6
4mw7
4mw9
4mwb
4mwc
4mwd
4mwe

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (13, 13)

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 3U1E: 2,2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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Related Entries

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Related Entries Specified in the PDB File