4MW7 - JenaLib

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Title :   TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-{3-[(5-CHLORO-2-ETHOXY-3-IODOBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA (CHEM 1469)

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 :   2.75

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, 21)

No.	Name	Count	Type	Full Name
1	2EF	1	Ligand/Ion	1-{3-[(5-CHLORO-2-ETHOXY-3-IODOBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
3	DMS	5	Ligand/Ion	DIMETHYL SULFOXIDE
4	GOL	11	Ligand/Ion	GLYCEROL
5	MET	1	Mod. Amino Acid	METHIONINE
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	2EF	-1	Ligand/Ion	1-{3-[(5-CHLORO-2-ETHOXY-3-IODOBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2	CAS	1	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 2 (5, 7)

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

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:271 , VAL A:275 , PRO A:718 , VAL A:722	BINDING SITE FOR RESIDUE GOL A 801
02	AC2	SOFTWARE	ILE A:265 , SER A:585 , GLY A:586 , PHE A:587 , PRO A:659 , ILE A:661 , GLN A:662	BINDING SITE FOR RESIDUE GOL A 802
03	AC3	SOFTWARE	TRP A:345 , GLU A:349 , TYR A:405 , PRO A:464 , GLY A:465	BINDING SITE FOR RESIDUE GOL A 803
04	AC4	SOFTWARE	ARG A:583 , ARG A:601	BINDING SITE FOR RESIDUE GOL A 804
05	AC5	SOFTWARE	PRO A:731 , GLU A:732 , VAL A:733	BINDING SITE FOR RESIDUE GOL A 805
06	AC6	SOFTWARE	GLY A:573 , TYR A:574 , ASP A:575 , ALA A:576 , LYS A:720	BINDING SITE FOR RESIDUE GOL A 806
07	AC7	SOFTWARE	GLU A:343 , LEU A:344 , ARG A:486 , ASP A:500 , PHE A:502	BINDING SITE FOR RESIDUE GOL A 807
08	AC8	SOFTWARE	ASN A:252 , HIS A:256 , LYS A:292 , SER A:366 , HIS A:395 , LYS A:550 , ASP A:551	BINDING SITE FOR RESIDUE GOL A 808
09	AC9	SOFTWARE	GLU A:392 , LYS A:517 , ASP A:518 , ILE A:519 , LEU A:520	BINDING SITE FOR RESIDUE DMS A 809
10	BC1	SOFTWARE	HOH A:961	BINDING SITE FOR RESIDUE DMS A 810
11	BC2	SOFTWARE	PHE A:370 , TYR A:526	BINDING SITE FOR RESIDUE DMS A 811
12	BC3	SOFTWARE	PHE A:319 , GLU A:320 , ILE A:326	BINDING SITE FOR RESIDUE DMS A 812
13	BC4	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 , THR A:549 , LYS A:550 , HOH A:944	BINDING SITE FOR RESIDUE MET A 813
14	BC5	SOFTWARE	GLU B:343 , LEU B:344 , ARG B:486	BINDING SITE FOR RESIDUE GOL B 801
15	BC6	SOFTWARE	ARG B:583 , ARG B:601	BINDING SITE FOR RESIDUE GOL B 802
16	BC7	SOFTWARE	TYR A:305 , HIS B:289 , LYS B:338 , ASN B:458 , ALA B:460 , CAS B:470	BINDING SITE FOR RESIDUE GOL B 803
17	BC8	SOFTWARE	GLU B:320 , TYR B:324 , ILE B:326	BINDING SITE FOR RESIDUE DMS B 804
18	BC9	SOFTWARE	TYR B:249 , TYR B:250 , HIS B:259 , 2EF B:806	BINDING SITE FOR RESIDUE SO4 B 805
19	CC1	SOFTWARE	PRO B:247 , ILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , TYR B:481 , ILE B:519 , PHE B:522 , HIS B:523 , SO4 B:805 , HOH B:999	BINDING SITE FOR RESIDUE 2EF B 806

(no "SS Bond" information available for 4MW7)

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 4MW7)

(no "PROSITE Motif" information available for 4MW7)

(no "Exon" information available for 4MW7)

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:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               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.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhh........................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mw7 A 239 EKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVGEVLFSKRST 767
                                   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   ||  566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756|      767
                                                                                                                                                                                                                                                                 470-CAS                                                                           552|                                                                                                                                                                                                756|         
                                                                                                                                                                                                                                                                                                                                                    561                                                                                                                                                                                                 758

Chain B from PDB  Type:PROTEIN  Length:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..............eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee........eee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhh.hhhhhh......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mw7 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371   ||  392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762     
                                0|                                                                                                                                       375|                                                                                470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                        387

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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 4MW7)

(no "CATH Domain" information available for 4MW7)

(no "Pfam Domain" information available for 4MW7)

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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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	4mw7
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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
4mw5
4mw6
4mw9
4mwb
4mwc
4mwd
4mwe

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 21)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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Exons (0, 0)

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