5IQD - JenaLib

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

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 :   2.20

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
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280

		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 (4, 19)

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
4	RIO	4	Ligand/Ion	RIBOSTAMYCIN

Biological Unit 1 (2, 2)

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
4	RIO	1	Ligand/Ion	RIBOSTAMYCIN

Biological Unit 2 (2, 2)

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
4	RIO	1	Ligand/Ion	RIBOSTAMYCIN

Biological Unit 3 (2, 2)

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
4	RIO	1	Ligand/Ion	RIBOSTAMYCIN

Biological Unit 4 (2, 2)

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
4	RIO	1	Ligand/Ion	RIBOSTAMYCIN

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:214 , ILE A:224 , LYS A:226 , TYR A:237 , 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:924 , HOH A:1038 , HOH A:1154 , HOH A:1206 , HOH A:1221	binding site for residue GNP A 500
02	AC2	SOFTWARE	ASP A:374 , SER A:376 , TYR A:408 , GLU A:411 , GLU A:415 , GLU A:416 , GLU A:445 , TYR A:448 , GLU A:451 , HOH A:972 , HOH A:1029 , HOH A:1045 , HOH A:1051 , HOH A:1160 , HOH A:1170 , HOH A:1302 , HOH A:1311 , HOH A:1426 , HOH A:1560	binding site for residue RIO A 600
03	AC3	SOFTWARE	HIS A:379 , ASP A:393 , GNP A:500 , HOH A:900 , HOH A:901	binding site for residue MG A 700
04	AC4	SOFTWARE	ASP A:393 , GNP A:500 , HOH A:902 , HOH A:903 , HOH A:904	binding site for residue MG A 702
05	AC5	SOFTWARE	GLN A:462 , ILE A:465 , ARG A:469 , HOH A:1107	binding site for residue CL A 802
06	AC6	SOFTWARE	SER B:214 , LYS B:226 , TYR B:237 , TYR B:274 , GLU B:276 , ILE B:277 , PHE B:281 , HIS B:379 , ILE B:392 , ASP B:393 , MG B:700 , MG B:702 , HOH B:900 , HOH B:901 , HOH B:903 , HOH B:904 , HOH B:906 , HOH B:909 , HOH B:923 , HOH B:924 , HOH B:1038 , HOH B:1093 , HOH B:1154 , HOH B:1206	binding site for residue GNP B 500
07	AC7	SOFTWARE	ASP B:374 , SER B:376 , TYR B:408 , GLU B:411 , GLU B:415 , GLU B:416 , VAL B:444 , GLU B:445 , GLU B:451 , HOH B:1029 , HOH B:1045 , HOH B:1051 , HOH B:1151 , HOH B:1160 , HOH B:1170 , HOH B:1260 , HOH B:1302 , HOH B:1311 , HOH B:1426 , HOH B:1560	binding site for residue RIO B 600
08	AC8	SOFTWARE	HIS B:379 , ASP B:393 , GNP B:500 , HOH B:900 , HOH B:901	binding site for residue MG B 700
09	AC9	SOFTWARE	ASP B:393 , GNP B:500 , HOH B:902 , HOH B:903 , HOH B:904	binding site for residue MG B 702
10	AD1	SOFTWARE	GLN B:462 , ILE B:465 , GLU B:466 , ARG B:469 , HOH B:1107	binding site for residue CL B 802
11	AD2	SOFTWARE	ILE C:208 , SER C:214 , ILE C:224 , LYS C:226 , TYR C:237 , TYR C:274 , GLU C:276 , ILE C:277 , PHE C:281 , HIS C:379 , ILE C:392 , 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:923 , HOH C:924 , HOH C:1038 , HOH C:1057 , HOH C:1124 , HOH C:1206 , HOH C:1221 , HOH C:1575	binding site for residue GNP C 500
12	AD3	SOFTWARE	ASP C:374 , SER C:376 , TYR C:408 , GLU C:411 , GLU C:415 , GLU C:416 , GLU C:445 , TYR C:448 , GLU C:451 , HOH C:1029 , HOH C:1045 , HOH C:1170 , HOH C:1260 , HOH C:1302 , HOH C:1426	binding site for residue RIO C 600
13	AD4	SOFTWARE	HIS C:379 , ASP C:393 , GNP C:500 , HOH C:900 , HOH C:901	binding site for residue MG C 700
14	AD5	SOFTWARE	ASP C:393 , GNP C:500 , HOH C:902 , HOH C:903 , HOH C:904	binding site for residue MG C 702
15	AD6	SOFTWARE	GLN C:462 , ARG C:469 , HOH C:1107	binding site for residue CL C 802
16	AD7	SOFTWARE	ILE D:208 , SER D:214 , LYS D:226 , TYR D:237 , TYR D:274 , GLU D:276 , ILE D:277 , PHE D:281 , HIS D:379 , ILE D:392 , ASP D:393 , MG D:700 , MG D:702 , HOH D:900 , HOH D:901 , HOH D:903 , HOH D:904 , HOH D:906 , HOH D:909 , HOH D:923 , HOH D:924 , HOH D:1038 , HOH D:1299	binding site for residue GNP D 500
17	AD8	SOFTWARE	ASP D:374 , SER D:376 , TYR D:408 , GLU D:411 , SER D:413 , GLU D:415 , GLU D:416 , VAL D:444 , GLU D:445 , TYR D:448 , GLU D:451 , HOH D:1029 , HOH D:1045 , HOH D:1051 , HOH D:1119 , HOH D:1126 , HOH D:1151 , HOH D:1160 , HOH D:1170 , HOH D:1302 , HOH D:1426	binding site for residue RIO D 600
18	AD9	SOFTWARE	HIS D:379 , ASP D:393 , GNP D:500 , HOH D:900 , HOH D:901	binding site for residue MG D 700
19	AE1	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 5IQD)

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

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

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

(no "Exon" information available for 5IQD)

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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeee....hhhhhhhhhhhhhhh........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
                 5iqd A 180 DDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   189       199       209       219       229||     243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      
                                                                            230|                                                                                                                                                                                                                                                    
                                                                             235

Chain B from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeee......hhhhhhhhhhhhhhh........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
                 5iqd B 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   188       198       208       218       228  ||   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
                                                                              231|                                                                                                                                                                                                                                                     
                                                                               234

Chain C from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeee...hhhhhhhhhhhhhhh........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
                 5iqd C 183 ATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   192       202       212       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  
                                                                        229|                                                                                                                                                                                                                                                    
                                                                         235

Chain D from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeeeee...eeeeee...eeeeee.....hhhhhhhhhhhhhhh........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
                 5iqd D 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   188       198       208       218       228 ||    241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       
                                                                             230|                                                                                                                                                                                                                                                    
                                                                              234

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(no "SCOP Domain" information available for 5IQD)

(no "CATH Domain" information available for 5IQD)

(no "Pfam Domain" information available for 5IQD)

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

5byl	5BYL CONTAINS THE SAME PROTEIN CO-CRYSTALLIZED WITH GMPPCP LIGAND
5iqa
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

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