5IQI - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   AMINOGLYCOSIDE PHOSPHOTRANSFERASE (2'')-IA (CTD OF AAC(6')-IE/APH(2'')-IA) Y237F MUTANT IN COMPLEX WITH GMPPNP AND MAGNESIUM

Authors :   S. J. Caldwell, A. M. Berghuis

Date :   10 Mar 16 (Deposition) - 25 May 16 (Release) - 15 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Kinase, Antibiotic, Aminoglycoside, Resistance, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Caldwell, Y. Huang, A. M. Berghuis
Antibiotic Binding Drives Catalytic Activation Of Aminoglycoside Kinase Aph(2)-Ia.
Structure V. 24 935 2016
PubMed-ID: 27161980 | Reference-DOI: 10.1016/J.STR.2016.04.002

Molecule 1 - BIFUNCTIONAL AAC/APH
	Chains	:	A, B, C, D
	EC Number	:	2.3.1.-, 2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-22B-APH(2'')-IA
	Expression System Strain	:	BL21(LDE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN (UNP RESIDUES 175-479)
	Gene	:	AACA-APHD, R015, VRA0030
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Other Details	:	C-TERMINAL DOMAIN OF AAC(6')-IE/APH(2'')-IA BIFUNCTIONAL ENZYME, RESIDUES 175-479

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	GNP	4	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	8	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:208 , GLY A:211 , SER A:214 , ALA A:216 , ILE A:224 , LYS A:226 , TYR A:274 , GLU A:276 , ILE A:277 , PHE A:281 , HIS A:379 , ILE A:392 , ASP A:393 , MG A:700 , MG A:702 , HOH A:900 , HOH A:901 , HOH A:903 , HOH A:904 , HOH A:906 , HOH A:923 , HOH A:1023 , HOH A:1038 , HOH A:1057 , HOH A:1083 , HOH A:1093 , HOH A:1154 , HOH A:1206 , HOH A:1221 , HOH A:1705	binding site for residue GNP A 500
02	AC2	SOFTWARE	HIS A:379 , ASP A:393 , GNP A:500 , HOH A:900 , HOH A:901	binding site for residue MG A 700
03	AC3	SOFTWARE	ASP A:393 , GNP A:500 , HOH A:902 , HOH A:903 , HOH A:904	binding site for residue MG A 702
04	AC4	SOFTWARE	GLN A:462 , ARG A:469	binding site for residue CL A 802
05	AC5	SOFTWARE	ILE B:208 , SER B:214 , ILE B:224 , LYS B:226 , TYR B:274 , GLU B:276 , ILE B:277 , PHE B:281 , ASP B:374 , HIS B:379 , ASP B:393 , MG B:700 , MG B:702 , HOH B:900 , HOH B:901 , HOH B:904 , HOH B:906 , HOH B:921 , HOH B:923 , HOH B:1093 , HOH B:1287	binding site for residue GNP B 500
06	AC6	SOFTWARE	HIS B:379 , ASP B:393 , GNP B:500 , MG B:702 , HOH B:900 , HOH B:901	binding site for residue MG B 700
07	AC7	SOFTWARE	ASP B:393 , GNP B:500 , MG B:700 , HOH B:902 , HOH B:903 , HOH B:904	binding site for residue MG B 702
08	AC8	SOFTWARE	GLN B:462 , ILE B:465 , GLU B:466 , ARG B:469	binding site for residue CL B 802
09	AC9	SOFTWARE	GLY C:211 , SER C:214 , ALA C:216 , ILE C:224 , LYS C:226 , PHE C:237 , TYR C:274 , GLU C:276 , ILE C:277 , PHE C:281 , HIS C:379 , ASP C:393 , MG C:700 , MG C:702 , HOH C:900 , HOH C:901 , HOH C:903 , HOH C:904 , HOH C:906 , HOH C:921 , HOH C:923 , HOH C:1038 , HOH C:1093 , HOH C:1142 , HOH C:1206 , HOH C:1221	binding site for residue GNP C 500
10	AD1	SOFTWARE	HIS C:379 , ASP C:393 , GNP C:500 , HOH C:900 , HOH C:901	binding site for residue MG C 700
11	AD2	SOFTWARE	ASP C:393 , GNP C:500 , HOH C:902 , HOH C:903 , HOH C:904	binding site for residue MG C 702
12	AD3	SOFTWARE	HOH B:1282 , GLN C:462 , ILE C:465 , ARG C:469 , HOH C:1107	binding site for residue CL C 802
13	AD4	SOFTWARE	ILE D:208 , SER D:214 , ALA D:216 , LYS D:226 , TYR D:274 , GLU D:276 , ILE D:277 , PHE D:281 , ASP D:374 , HIS D:379 , ILE D:392 , ASP D:393 , MG D:700 , MG D:702 , HOH D:900 , HOH D:901 , HOH D:902 , HOH D:904 , HOH D:906 , HOH D:921 , HOH D:923 , HOH D:1035 , HOH D:1057 , HOH D:1093 , HOH D:1119	binding site for residue GNP D 500
14	AD5	SOFTWARE	HIS D:379 , ASP D:393 , GNP D:500 , HOH D:900 , HOH D:901	binding site for residue MG D 700
15	AD6	SOFTWARE	ASP D:393 , GNP D:500 , HOH D:902 , HOH D:903 , HOH D:904	binding site for residue MG D 702

(no "SS Bond" information available for 5IQI)

(no "Cis Peptide Bond" information available for 5IQI)

(no "SAP(SNP)/Variant" information available for 5IQI)

(no "PROSITE Motif" information available for 5IQI)

(no "Exon" information available for 5IQI)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeee......hhhhhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqi A 182 NATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGFAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471

Chain B from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeee...hhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iqi B 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSFAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   188       198       208       218       228 ||    244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474    
                                                                             230|                                                                                                                                                                                                                                                 
                                                                              237

Chain C from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeeee.....hhhhhhhhhhhhhhhhh........eeeeee...eeeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqi C 183 ATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGFAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472

Chain D from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeeee.eeeee...eeeeee....hhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqi D 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSVAYLVNNEYIFKTKFSTFAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   188       198       208||     222       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477 
                                                        209|              231|                                                                                                                                                                                                                                                 
                                                         214               237

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	AACA_STAAU \| P0A0C1	:	4ork 5byl 5iqa 5iqb 5iqc 5iqd 5iqe 5iqf 5iqg 5iqh

Description

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Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

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