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(-) Description

Title :  CRYSTAL STRUCTURE OF ELONGATION FACTOR, TU (EF-TU-MGGDP) COMPLEXED WITH GE2270A, A THIAZOLYL PEPTIDE ANTIBIOTIC
 
Authors :  S. E. Heffron, F. Jurnak
Date :  25 Oct 99  (Deposition) - 25 Oct 00  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase-Antibiotic Complex, Thiopeptide, Antibiotic, Antibacterial, Thiazole, Oxazole, Hydrolase, Gtpase, Translation Elongation Factor, Protein Synthesis, Nucleotide-Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Heffron, F. Jurnak
Structure Of An Ef-Tu Complex With A Thiazolyl Peptide Antibiotic Determined At 2. 35 A Resolution: Atomic Basis Fo Ge2270A Inhibition Of Ef-Tu.
Biochemistry V. 39 37 2000
PubMed-ID: 10625477  |  Reference-DOI: 10.1021/BI9913597

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU
    Chains: A, B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - THIOCILLIN GE2270
    Chains: C, D
    Organism Scientific: PLANOBISPORA ROSEA
    Organism Taxid: 35762
    Synonym: GE2270A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 54)

Asymmetric Unit (10, 54)
No.NameCountTypeFull Name
1ACT30Ligand/IonACETATE ION
2BB62Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
3BB72Mod. Amino Acid(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID
4BB82Mod. Amino Acid(2S,3S)-BETA-HYDROXY-PHENYLALANINE
5BB98Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
6GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
7MEN2Mod. Amino AcidN-METHYL ASPARAGINE
8MG2Ligand/IonMAGNESIUM ION
9MH62Mod. Amino Acid3-HYDROXY-2-IMINOPROPANOIC ACID
10NH22Mod. Amino AcidAMINO GROUP
Biological Unit 1 (9, 30)
No.NameCountTypeFull Name
1ACT19Ligand/IonACETATE ION
2BB61Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
3BB71Mod. Amino Acid(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID
4BB81Mod. Amino Acid(2S,3S)-BETA-HYDROXY-PHENYLALANINE
5BB94Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
6GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
7MEN1Mod. Amino AcidN-METHYL ASPARAGINE
8MG-1Ligand/IonMAGNESIUM ION
9MH61Mod. Amino Acid3-HYDROXY-2-IMINOPROPANOIC ACID
10NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (9, 22)
No.NameCountTypeFull Name
1ACT11Ligand/IonACETATE ION
2BB61Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
3BB71Mod. Amino Acid(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID
4BB81Mod. Amino Acid(2S,3S)-BETA-HYDROXY-PHENYLALANINE
5BB94Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
6GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
7MEN1Mod. Amino AcidN-METHYL ASPARAGINE
8MG-1Ligand/IonMAGNESIUM ION
9MH61Mod. Amino Acid3-HYDROXY-2-IMINOPROPANOIC ACID
10NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:25 , GDP A:999 , HOH A:2018 , HOH A:2063 , HOH A:2064 , HOH A:2218BINDING SITE FOR RESIDUE MG A 998
02AC2SOFTWAREASP 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:998 , HOH A:2017 , HOH A:2063 , HOH A:2064 , HOH A:2217 , HOH A:2218 , HOH A:2219BINDING SITE FOR RESIDUE GDP A 999
03AC3SOFTWARETHR A:167 , PRO A:168 , ILE A:169 , HOH A:2115 , ACT A:3019BINDING SITE FOR RESIDUE ACT A 3002
04AC4SOFTWAREARG A:123 , ASP A:370 , ALA A:389BINDING SITE FOR RESIDUE ACT A 3003
05AC5SOFTWAREARG A:154 , ASP A:165 , SER A:221 , ACT A:3028BINDING SITE FOR RESIDUE ACT A 3004
06AC6SOFTWAREGLU A:152 , GLU A:155 , GLN A:159 , HOH A:2221BINDING SITE FOR RESIDUE ACT A 3005
07AC7SOFTWARETHR A:302 , LEU A:362 , ILE A:363 , HOH A:2172BINDING SITE FOR RESIDUE ACT A 3006
08AC8SOFTWAREVAL A:127 , ARG A:373BINDING SITE FOR RESIDUE ACT A 3007
09AC9SOFTWAREPRO A:113 , HOH A:2221 , HOH A:2222 , ACT B:3009BINDING SITE FOR RESIDUE ACT A 3010
10BC1SOFTWAREARG A:171 , TRP A:184 , HOH A:2223 , ACT A:3023BINDING SITE FOR RESIDUE ACT A 3013
11BC2SOFTWAREILE A:247 , GLU A:287BINDING SITE FOR RESIDUE ACT A 3016
12BC3SOFTWAREVAL A:391 , LEU A:392BINDING SITE FOR RESIDUE ACT A 3017
13BC4SOFTWAREILE A:169 , VAL A:170 , ARG A:171 , LYS A:187 , GLU A:190 , ACT A:3002BINDING SITE FOR RESIDUE ACT A 3019
14BC5SOFTWAREGLU A:6 , GLY A:94 , ALA A:95BINDING SITE FOR RESIDUE ACT A 3020
15BC6SOFTWAREASP A:50 , PRO A:82 , HOH A:2017BINDING SITE FOR RESIDUE ACT A 3021
16BC7SOFTWARESER A:65 , HIS A:66BINDING SITE FOR RESIDUE ACT A 3022
17BC8SOFTWAREVAL A:140 , ASP A:141 , ASP A:142 , GLU A:143 , LEU A:146 , ACT A:3013 , BB9 C:2BINDING SITE FOR RESIDUE ACT A 3023
18BC9SOFTWARETYR A:129 , TYR A:198 , HOH A:2226 , HOH A:2227BINDING SITE FOR RESIDUE ACT A 3025
19CC1SOFTWAREHIS A:84 , ASN A:355BINDING SITE FOR RESIDUE ACT A 3026
20CC2SOFTWAREILE A:220 , SER A:221 , ACT A:3004BINDING SITE FOR RESIDUE ACT A 3028
21CC3SOFTWARETYR A:39 , LEU A:189 , ALA A:192 , ASP A:196BINDING SITE FOR RESIDUE ACT A 3030
22CC4SOFTWARETHR B:25 , ASP B:50 , GDP B:999 , HOH B:2006 , HOH B:2013 , HOH B:2140 , HOH B:2141BINDING SITE FOR RESIDUE MG B 998
23CC5SOFTWAREASP 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 , SER B:173 , ALA B:174 , LEU B:175 , MG B:998 , HOH B:2004 , HOH B:2139 , HOH B:2140 , HOH B:2141BINDING SITE FOR RESIDUE GDP B 999
24CC6SOFTWAREARG B:154 , ILE B:169 , ACT B:3008BINDING SITE FOR RESIDUE ACT B 3001
25CC7SOFTWAREVAL B:170 , ARG B:171 , LYS B:187 , GLU B:190 , ACT B:3001BINDING SITE FOR RESIDUE ACT B 3008
26CC8SOFTWAREPRO A:111 , ACT A:3010 , ARG B:318 , HIS B:319 , THR B:320 , GLU B:378BINDING SITE FOR RESIDUE ACT B 3009
27CC9SOFTWAREPHE A:323 , GLU A:348 , VAL B:140 , ASP B:141 , ASP B:142BINDING SITE FOR RESIDUE ACT B 3011
28DC1SOFTWAREGLU B:215 , ARG B:288 , TYR B:331 , ARG B:333 , HOH B:2087BINDING SITE FOR RESIDUE ACT B 3012
29DC2SOFTWAREHIS B:84 , GLY B:353 , ASN B:355BINDING SITE FOR RESIDUE ACT B 3014
30DC3SOFTWAREGLY B:41 , ALA B:42 , GLU B:68 , ASP B:70 , HOH B:2008BINDING SITE FOR RESIDUE ACT B 3015
31DC4SOFTWAREASP B:166BINDING SITE FOR RESIDUE ACT B 3018
32DC5SOFTWAREGLU B:201 , HOH B:2144BINDING SITE FOR RESIDUE ACT B 3024
33DC6SOFTWAREASP B:336BINDING SITE FOR RESIDUE ACT B 3027
34DC7SOFTWARETYR B:39 , LEU B:189 , ASP B:196 , HOH B:2145 , HOH B:2146BINDING SITE FOR RESIDUE ACT B 3029
35DC8SOFTWAREGLY A:222 , PRO C:14BINDING SITE FOR RESIDUE NH2 C 15
36DC9SOFTWAREGLY B:222 , SER D:13 , PRO D:14BINDING SITE FOR RESIDUE NH2 D 15
37EC1SOFTWARETHR A:73 , GLU A:143 , ALA A:182 , GLU A:215 , ASP A:216 , GLY A:222 , ARG A:223 , VAL A:226 , THR A:228 , GLY A:229 , ARG A:230 , THR A:256 , GLY A:257 , VAL A:258 , GLU A:259 , PHE A:261 , ARG A:262 , ASN A:273 , VAL A:274 , GLY A:275 , LEU A:277 , HOH A:2024 , HOH A:2161 , ACT A:3023 , NH2 C:15 , HOH C:2002 , HOH C:2003BINDING SITE FOR CHAIN C OF THIOCILIN GE2270
38EC2SOFTWAREPRO B:72 , THR B:73 , GLU B:143 , GLU B:215 , ASP B:216 , PHE B:218 , ARG B:223 , VAL B:226 , THR B:228 , ARG B:230 , THR B:256 , GLY B:257 , VAL B:258 , GLU B:259 , PHE B:261 , ARG B:262 , LEU B:264 , ASN B:273 , VAL B:274 , GLY B:275 , LEU B:277 , HOH B:2097 , HOH B:2099 , NH2 D:15 , HOH D:2001BINDING SITE FOR CHAIN D OF THIOCILIN GE2270

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D8T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D8T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D8T)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU1_ECOLI51-66
 		  2A:50-65
B:50-65
EFTU2_ECOLI51-66
 		  2A:50-65
B:50-65
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU1_ECOLI51-66
 		  1A:50-65
-
EFTU2_ECOLI51-66
 		  1A:50-65
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU1_ECOLI51-66
 		  1-
B:50-65
EFTU2_ECOLI51-66
 		  1-
B:50-65

(-) Exons   (0, 0)

(no "Exon" information available for 1D8T)

(-) Sequences/Alignments

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:391
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:391
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393 
          EFTU1_ECOLI     4 EKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d1d8ta3 A:3-204 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                       d1d8ta1 A:205-296 Elongation factor Tu (EF-Tu), domain 2                                    d1d8ta2 A:297-393 Elongation factor Tu (EF-Tu)                                                    SCOP domains
               CATH domains ------1d8tA01 A:9-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              --1d8tA02 A:205-299 Translation factors                                                          1d8tA03 A:300-392 Translation factors                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhh..eeee..eeee.eeeeee....eeeeee..hhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh..hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee..eeeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee...........ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8t A   3 EKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    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 


Chain A from PDB  Type:PROTEIN  Length:391
 aligned with EFTU2_ECOLI | P0CE48 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:391
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393 
          EFTU2_ECOLI     4 EKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 394
               SCOP domains d1d8ta3 A:3-204 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                       d1d8ta1 A:205-296 Elongation factor Tu (EF-Tu), domain 2                                    d1d8ta2 A:297-393 Elongation factor Tu (EF-Tu)                                                    SCOP domains
               CATH domains ------1d8tA01 A:9-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              --1d8tA02 A:205-299 Translation factors                                                          1d8tA03 A:300-392 Translation factors                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhh..eeee..eeee.eeeeee....eeeeee..hhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh..hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee..eeeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee...........ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8t A   3 EKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    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 


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:385
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389     
          EFTU1_ECOLI    10 KPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d1d8tb3 B:9-204 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                 d1d8tb1 B:205-296 Elongation factor Tu (EF-Tu), domain 2                                    d1d8tb2 B:297-393 Elongation factor Tu (EF-Tu)                                                    SCOP domains
               CATH domains 1d8tB01 B:9-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              --1d8tB02 B:205-298 Translation factors                                                         1d8tB03 B:299-392 Translation factors                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhh..ee......ee.eeeeee....eeeeee..hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhhhh...hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee..eeeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee...........ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8t B   9 KPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    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     


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with EFTU2_ECOLI | P0CE48 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:385
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389     
          EFTU2_ECOLI    10 KPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 394
               SCOP domains d1d8tb3 B:9-204 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                 d1d8tb1 B:205-296 Elongation factor Tu (EF-Tu), domain 2                                    d1d8tb2 B:297-393 Elongation factor Tu (EF-Tu)                                                    SCOP domains
               CATH domains 1d8tB01 B:9-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              --1d8tB02 B:205-298 Translation factors                                                         1d8tB03 B:299-392 Translation factors                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhh..ee......ee.eeeeee....eeeeee..hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhhhh...hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee..eeeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee...........ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8t B   9 KPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    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     


Chain C from PDB  Type:PROTEIN  Length:15
 aligned with THCL_PLARO | Q7M0J8 from UniProtKB/Swiss-Prot  Length:14

    Alignment length:15
                                        14 
                                    10   | 
           THCL_PLARO     1 SCNCVCGFCCSCSP-   -
               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
                 1d8t C   1 ScncVcGfccscSPx  15
                             ||| | |10||  |
                             2-BB9 |||||  |
                              3-MEN|||||  |
                               4-BB6||||  |
                                 6-BB7||  |
                                   8-BB8  |
                                    9-BB9 |
                                    10-BB9|
                                     11-MH6
                                      12-BB9


Chain D from PDB  Type:PROTEIN  Length:15
 aligned with THCL_PLARO | Q7M0J8 from UniProtKB/Swiss-Prot  Length:14

    Alignment length:15
                                        14  
                                    10   | 
           THCL_PLARO     1 SCNCVCGFCCSCSP-   -
               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
                 1d8t D   1 ScncVcGfccscSPx  15
                             ||| | |10||  |
                             ||| | |||12-BB9
                             2-BB9 ||||  15-NH2
                              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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D8T)

(-) Gene Ontology  (17, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EFTU2_ECOLI | P0CE48)
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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 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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  1d8t
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EFTU1_ECOLI | P0CE47: 1dg1 1efc 1efm 1efu 1etu 1ls2 1mj1 1qzd 2bvn 2fx3 2hcj 2hdn 3ep2 3eq3 3eq4 3u2q 3u6b 3u6k 4g5g 4pc3 4pc7 4q7j 4v69 5jbq
        EFTU2_ECOLI | P0CE48: 1dg1 1efc 1efm 1efu 1etu 1ls2 1ob2 1qzd 2bvn 2hcj 2hdn 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3ep2 3eq3 3eq4 3mmp 3vnu 3vnv 4fwt 4r71 4v69 4v6k 4v6l 5afi
        THCL_PLARO | Q7M0J8: 2c77 3u2q 3u6b 3u6k

(-) Related Entries Specified in the PDB File

1e9w CRYSTAL STRUCTURE OF THIOPEPTIDE THIOSTREPTON
1oln SOLUTION STRUCTURE OF THIOPEPTIDE THIOSTREPTON BINDING TO L11 SUBSTRATE FROM 50S RIBOSOMAL RNA
2c77 CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-GNP COMPLEXED WITH THIOPEPTIDE GE2270A.
2jq7 SOLUTION STRUCTURE OF THE COMPLEX OF THIOPEPTIDE THIOSTREPTON AND RIBOSOMAL L11-RNA
2zjp CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
3cf5 CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE THIOPEPTIDE THIOSTREPTON