3U6B - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LDI028

Authors :   D. J. Palestrant

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

Method :   X-RAY DIFFRACTION

Resolution :   2.12

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 Strain	:	BL21 (STAR)
	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-LDI028
	Chains	:	C, D
	Engineered	:	YES
	Synonym	:	EF-TU 1, P-43 ,EF-TU
	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	8BB	2	Mod. Amino Acid	TRANS-4-{[(E)-1-AMINO-2-SULFANYLETHENYL]CARBAMOYL}CYCLOHEXANECARBOXYLIC ACID
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	8BB	1	Mod. Amino Acid	TRANS-4-{[(E)-1-AMINO-2-SULFANYLETHENYL]CARBAMOYL}CYCLOHEXANECARBOXYLIC ACID
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	8BB	1	Mod. Amino Acid	TRANS-4-{[(E)-1-AMINO-2-SULFANYLETHENYL]CARBAMOYL}CYCLOHEXANECARBOXYLIC ACID
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	THR A:25 , GDP A:402 , HOH A:503 , HOH A:514 , HOH A:517 , HOH A:531	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	ASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , ASN A:135 , LYS A:136 , ASP A:138 , MET A:139 , SER A:173 , ALA A:174 , LEU A:175 , MG A:401 , HOH A:514 , HOH A:517 , HOH A:554 , HOH A:562	BINDING SITE FOR RESIDUE GDP A 402
3	AC3	SOFTWARE	HIS B:19 , ASP B:21 , HIS B:22 , GLY B:23 , LYS B:24 , THR B:25 , THR B:26 , ASN B:135 , LYS B:136 , ASP B:138 , MET B:139 , SER B:173 , ALA B:174 , LEU B:175 , MG B:402 , HOH B:505 , HOH B:509 , HOH B:512 , HOH B:514 , HOH B:515	BINDING SITE FOR RESIDUE GDP B 401
4	AC4	SOFTWARE	THR B:25 , GDP B:401 , HOH B:505 , HOH B:512 , HOH B:514 , HOH B:516	BINDING SITE FOR RESIDUE MG B 402
5	AC5	SOFTWARE	GLU B:143 , GLU B:215 , ASP B:216 , PHE B:218 , VAL B:226 , THR B:228 , THR B:256 , GLY B:257 , GLU B:259 , PHE B:261 , ARG B:262 , ARG B:269 , ASN B:273 , VAL B:274 , GLY B:275 , LEU B:277 , HOH C:101	BINDING SITE FOR CHAIN C OF NVP-LDI028
6	AC6	SOFTWARE	GLU A:143 , ILE A:206 , GLU A:215 , ASP A:216 , PHE A:218 , THR A:228 , THR A:256 , GLY A:257 , GLU A:259 , MET A:260 , PHE A:261 , ARG A:262 , ARG A:269 , ASN A:273 , VAL A:274 , GLY A:275 , LEU A:277	BINDING SITE FOR CHAIN D OF NVP-LDI028

(no "SS Bond" information available for 3U6B)

Asymmetric Unit

No.	Residues
1	Ala B:95	-	Ala B:96

(no "SAP(SNP)/Variant" information available for 3U6B)

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:58-65 B:56-65

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:58-65 -

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:56-65

(no "Exon" information available for 3U6B)

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:369
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:389
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385         
          EFTU1_ECOLI     6 FERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d3u6ba1 A:5-204 automated matches                                                                                                                                                                       d3u6ba2 A:205-29    6 automated matches                                                     d3u6ba3 A:297-393 automated matches                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.....hhhhhhhhhhhhhhhhh..----------------.......eeeeee....eeeeee..hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhh..hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee...ee..----.eeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee.hhhhh.....ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u6b A   5 FERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGG----------------RGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSI----TVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    14        24        34      |  -         -   |    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     |   -|      234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384         
                                                               41               58                                                                                                                                                               220  225

Chain B from PDB  Type:PROTEIN  Length:376
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:392
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392  
          EFTU1_ECOLI     3 KEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d3u6bb1 B:2-204 automated matches                                                                                                                                                                          d3u6bb2 B:205-29    6 automated matches                                                     d3u6bb3 B:297-393 automated matches                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhh...------------.........eeeeee....eeeeee..hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhh..hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee...ee..----.eeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeeee..hhhhh....eee.....eeeeeeeeeeee.hhhhh............eeee..eeeeeeee............eeeeeeeeeeeeee....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u6b B   2 KEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAA------------KARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSI----TVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    11        21        31        41 |       -    |   61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        |-   |   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  
                                                                    43           56                                                                                                                                                                 220  225

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
                 3u6b C   1 ScncVcGfccsx  12
                             ||| | |10||
                             2-BB9 |||||
                              3-MEN|||||
                               4-BB6||||
                                 6-BB7||
                                   8-BB8
                                    9-BB9
                                    10-BB9
                                     11-MH6
                                      12-8BB

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
                 3u6b D   1 ScncVcGfccsx  12
                             ||| | |10||
                             ||| | |||12-8BB
                             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 3U6B)

(no "Pfam Domain" information available for 3U6B)

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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	Cis Peptide Bonds
		Ala B:95 - Ala B:96	[ RasMol ]

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	3u6b
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3u2q	EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LFF571
3u6k	EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH NVP-LDK733

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 22)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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