4MWD - JenaLib

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Title :   TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA (CHEM 1433) AND ATP ANALOG AMPPCP

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 :   2.25

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 (7, 21)

No.	Name	Count	Type	Full Name
1	43E	1	Ligand/Ion	1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
3	CAS	4	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
4	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
5	GOL	9	Ligand/Ion	GLYCEROL
6	MET	1	Mod. Amino Acid	METHIONINE
7	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 10)

No.	Name	Count	Type	Full Name
1	43E	-1	Ligand/Ion	1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2	ACP	-1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
3	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
4	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
5	GOL	4	Ligand/Ion	GLYCEROL
6	MET	1	Mod. Amino Acid	METHIONINE
7	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (6, 11)

No.	Name	Count	Type	Full Name
1	43E	1	Ligand/Ion	1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
3	CAS	2	Mod. Amino Acid	S-(DIMETHYLARSENIC)CYSTEINE
4	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
5	GOL	5	Ligand/Ion	GLYCEROL
6	MET	-1	Mod. Amino Acid	METHIONINE
7	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:345 , GLU A:349 , PRO A:464 , GLY A:465 , ASN A:466	BINDING SITE FOR RESIDUE GOL A 901
02	AC2	SOFTWARE	ARG A:583 , ARG A:601	BINDING SITE FOR RESIDUE GOL A 902
03	AC3	SOFTWARE	HIS A:289 , LYS A:338 , ASN A:458 , TRP A:459 , ALA A:460 , HOH A:1118	BINDING SITE FOR RESIDUE GOL A 903
04	AC4	SOFTWARE	ARG A:719	BINDING SITE FOR RESIDUE GOL A 904
05	AC5	SOFTWARE	VAL A:436 , HOH A:1225	BINDING SITE FOR RESIDUE DMS A 905
06	AC6	SOFTWARE	PHE A:370 , LYS A:521 , TYR A:526 , HOH A:1056	BINDING SITE FOR RESIDUE DMS A 906
07	AC7	SOFTWARE	ARG A:271 , VAL A:275 , SER A:714 , PRO A:718	BINDING SITE FOR RESIDUE SO4 A 907
08	AC8	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:1100 , HOH A:1116	BINDING SITE FOR RESIDUE MET A 908
09	AC9	SOFTWARE	GLU B:343 , LEU B:482 , ARG B:486 , HOH B:1140	BINDING SITE FOR RESIDUE GOL B 801
10	BC1	SOFTWARE	ARG B:583 , ARG B:601 , HOH B:1043	BINDING SITE FOR RESIDUE GOL B 802
11	BC2	SOFTWARE	TYR B:472 , PHE B:522 , 43E B:808 , HOH B:1089 , HOH B:1160 , HOH B:1161	BINDING SITE FOR RESIDUE GOL B 803
12	BC3	SOFTWARE	GLU B:239 , TYR B:359 , PHE B:370 , ASN B:404 , MET B:406 , HOH B:928	BINDING SITE FOR RESIDUE GOL B 804
13	BC4	SOFTWARE	HIS B:289 , THR B:333 , LYS B:338 , ASN B:458 , TRP B:459 , ALA B:460	BINDING SITE FOR RESIDUE GOL B 805
14	BC5	SOFTWARE	GLU B:320 , TYR B:324 , ILE B:326 , HOH B:1002	BINDING SITE FOR RESIDUE DMS B 806
15	BC6	SOFTWARE	ARG B:271 , VAL B:275 , SER B:714 , PRO B:718 , HOH B:1139	BINDING SITE FOR RESIDUE SO4 B 807
16	BC7	SOFTWARE	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 , ALA B:477 , TYR B:481 , HIS B:523 , GOL B:803 , ACP B:809 , HOH B:960 , HOH B:965	BINDING SITE FOR RESIDUE 43E B 808
17	BC8	SOFTWARE	TYR B:249 , TYR B:250 , GLY B:258 , HIS B:259 , SER B:262 , GLY B:516 , ASP B:518 , HIS B:545 , GLY B:546 , TRP B:547 , TRP B:548 , 43E B:808 , HOH B:925 , HOH B:1064 , HOH B:1123 , HOH B:1154 , HOH B:1163	BINDING SITE FOR RESIDUE ACP B 809

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

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 4MWD)

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

(no "Exon" information available for 4MWD)

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..eeeeeehhhhhhhhhhhhhh.eee.....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
                 4mwd 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 
                                                                                                          318-CAS                                                                                                                                                 470-CAS

Chain B from PDB  Type:PROTEIN  Length:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeee....eeee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.hhhh...eee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee..ee.........hhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhh.hhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mwd B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311      |321       331       341       351       361       371       381|      394       404       414       424       434       444       454       464     | 474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764   
                                0|                                                                              318-CAS                                                        381|                                                                                  470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                              385

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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 4MWD)

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

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

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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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	4mwd
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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
4mw7
4mw9
4mwb
4mwc
4mwe

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 21)

Sites (17, 17)

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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