3U6K - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LDK733

Authors :   D. J. Palestrant

Date :   12 Oct 11 (Deposition) - 08 Feb 12 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Translation Factor-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Lamarche, J. A. Leeds, K. Amaral, J. T. Brewer, S. M. Bushell, J. M. Dewhurst, J. Dzink-Fox, E. Gangl, J. Goldovitz, A. Jain, S. Mullin, G. Neckermann, C. Osborne, D. Palestrant, M. A. Patane, E. M. Rann, M. Sachdeva, J. Shao, S. Tiamfook, L. Whitehead, D. Yu
Antibacterial Optimization Of 4-Aminothiazolyl Analogues Of The Natural Product Ge2270 A: Identification Of The Cycloalkylcarboxylic Acids.
J. Med. Chem. V. 54 8099 2011
PubMed-ID: 21999529 | Reference-DOI: 10.1021/JM200938F

Molecule 1 - ELONGATION FACTOR TU 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TUFA, B3339, JW3301
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	EF-TU 1, P-43

Molecule 2 - THIOCILLIN GE2270 ANALOGUE NVP-LDK733
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (9, 22)

No.	Name	Count	Type	Full Name
1	9BB	2	Mod. Amino Acid	TRANS-4-({[(E)-1-AMINO-2-SULFANYLETHENYL]CARBAMOYL}OXY)CYCLOHEXANECARBOXYLICACID
2	BB6	2	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
3	BB7	2	Mod. Amino Acid	(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID
4	BB8	2	Mod. Amino Acid	(2S,3S)-BETA-HYDROXY-PHENYLALANINE
5	BB9	6	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
6	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
7	MEN	2	Mod. Amino Acid	N-METHYL ASPARAGINE
8	MG	2	Ligand/Ion	MAGNESIUM ION
9	MH6	2	Mod. Amino Acid	3-HYDROXY-2-IMINOPROPANOIC ACID

Biological Unit 1 (8, 10)

No.	Name	Count	Type	Full Name
1	9BB	1	Mod. Amino Acid	TRANS-4-({[(E)-1-AMINO-2-SULFANYLETHENYL]CARBAMOYL}OXY)CYCLOHEXANECARBOXYLICACID
2	BB6	1	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
3	BB7	1	Mod. Amino Acid	(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID
4	BB8	1	Mod. Amino Acid	(2S,3S)-BETA-HYDROXY-PHENYLALANINE
5	BB9	3	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
6	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
7	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE
8	MG	-1	Ligand/Ion	MAGNESIUM ION
9	MH6	1	Mod. Amino Acid	3-HYDROXY-2-IMINOPROPANOIC ACID

Biological Unit 2 (8, 10)

No.	Name	Count	Type	Full Name
1	9BB	1	Mod. Amino Acid	TRANS-4-({[(E)-1-AMINO-2-SULFANYLETHENYL]CARBAMOYL}OXY)CYCLOHEXANECARBOXYLICACID
2	BB6	1	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
3	BB7	1	Mod. Amino Acid	(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID
4	BB8	1	Mod. Amino Acid	(2S,3S)-BETA-HYDROXY-PHENYLALANINE
5	BB9	3	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
6	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
7	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE
8	MG	-1	Ligand/Ion	MAGNESIUM ION
9	MH6	1	Mod. Amino Acid	3-HYDROXY-2-IMINOPROPANOIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , PHE A:46 , ASN A:135 , LYS A:136 , ASP A:138 , MET A:139 , SER A:173 , ALA A:174 , LEU A:175 , MG A:394 , HOH A:439 , HOH A:441 , HOH A:444 , ASP B:47 , ASN B:51	BINDING SITE FOR RESIDUE GDP A 500
2	AC2	SOFTWARE	THR A:25 , CYS A:81 , HOH A:439 , HOH A:441 , HOH A:442 , HOH A:444 , GDP A:500	BINDING SITE FOR RESIDUE MG A 394
3	AC3	SOFTWARE	HIS B:19 , ASP B:21 , HIS B:22 , GLY B:23 , LYS B:24 , THR B:25 , THR B:26 , PHE B:46 , ASN B:135 , LYS B:136 , ASP B:138 , MET B:139 , ALA B:174 , MG B:394 , HOH B:395 , HOH B:396 , HOH B:403	BINDING SITE FOR RESIDUE GDP B 500
4	AC4	SOFTWARE	THR B:25 , HOH B:395 , HOH B:396 , HOH B:397 , HOH B:403 , GDP B:500	BINDING SITE FOR RESIDUE MG B 394
5	AC5	SOFTWARE	GLU A:215 , ASP A:216 , PHE A:218 , ILE A:220 , THR A:228 , THR A:256 , GLY A:257 , GLU A:259 , PHE A:261 , ARG A:262 , ASN A:273 , VAL A:274 , GLY A:275 , LEU A:277 , ARG A:381 , HOH A:402 , THR B:38 , TYR B:39 , ARG B:318 , THR B:320 , PRO B:321 , PHE B:323 , HOH B:423 , HOH C:18	BINDING SITE FOR CHAIN C OF NVP-LDK733
6	AC6	SOFTWARE	TYR A:39 , PRO A:72 , THR A:320 , PRO A:321 , PHE A:323 , TYR A:326 , HOH A:448 , GLU B:215 , ASP B:216 , ARG B:223 , THR B:228 , GLY B:257 , VAL B:258 , GLU B:259 , PHE B:261 , ASN B:273 , VAL B:274 , GLY B:275 , LEU B:277 , HOH B:447 , HOH D:13 , HOH D:143	BINDING SITE FOR CHAIN D OF NVP-LDK733

(no "SS Bond" information available for 3U6K)

(no "Cis Peptide Bond" information available for 3U6K)

(no "SAP(SNP)/Variant" information available for 3U6K)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EFTU1_ECOLI	51-66	2	A:50-65 B:50-65

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EFTU1_ECOLI	51-66	1	A:50-65 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EFTU1_ECOLI	51-66	1	- B:50-65

(no "Exon" information available for 3U6K)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:386
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:386
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      
          EFTU1_ECOLI     9 TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d3u6ka1 A:8-204 automated matches                                                                                                                                                                    d3u6ka2 A:205-296 automated matches                                                         d3u6ka3 A:297-393 automated matches                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhhh.....hhhhhhh..eeee..eeee.eeeeee....eeeeee..hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh...hhhhhhhhhhhhhhhhh..hhhhh.eee.hhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhh..eee...eeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee......eeeeeeeeeee.hhhhh.....ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeee.....eeeee....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u6k A   8 TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387

Chain B from PDB  Type:PROTEIN  Length:386
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:386
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      
          EFTU1_ECOLI     9 TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d3u6kb1 B:8-204 automated matches                                                                                                                                                                    d3u6kb2 B:205-296 automated matches                                                         d3u6kb3 B:297-393 automated matches                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhhh..............eee....eee.eeeeeee..eeeeeee..hhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhh.........eee.hhhhhhhh...hhhhhhhhhhhhhhhh...........eee...eeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeeee..hhhhh....eee......eeeeeeeeeee.hhhhh............eeee..eeeeeeee............eeeeeeeeeeeee.....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u6k B   8 TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387

Chain C from PDB  Type:PROTEIN  Length:12
 aligned with THCL_PLARO | Q7M0J8 from UniProtKB/Swiss-Prot  Length:14

    Alignment length:12
                                    10  
           THCL_PLARO     1 SCNCVCGFCCSC  12
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3u6k C   1 ScncVcGfccsx  12
                             ||| | |10||
                             2-BB9 |||||
                              3-MEN|||||
                               4-BB6||||
                                 6-BB7||
                                   8-BB8
                                    9-BB9
                                    10-BB9
                                     11-MH6
                                      12-9BB

Chain D from PDB  Type:PROTEIN  Length:12
 aligned with THCL_PLARO | Q7M0J8 from UniProtKB/Swiss-Prot  Length:14

    Alignment length:12
                                    10  
           THCL_PLARO     1 SCNCVCGFCCSC  12
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3u6k D   1 ScncVcGfccsx  12
                             ||| | |10||
                             ||| | |||12-9BB
                             2-BB9 |||| 
                              3-MEN|||| 
                               4-BB6||| 
                                 6-BB7| 
                                   8-BB8
                                    9-BB9
                                    10-BB9
                                     11-MH6

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 "CATH Domain" information available for 3U6K)

(no "Pfam Domain" information available for 3U6K)

Asymmetric Unit(hide GO term definitions)

Chain A,B (EFTU1_ECOLI | P0CE47)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D (THCL_PLARO | Q7M0J8)

biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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3u2q	EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LFF571
3u6b	EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LDI028

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 22)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File