5IQE - JenaLib

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

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 :   2.50

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, 17)

No.	Name	Count	Type	Full Name
1	GNP	4	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	8	Ligand/Ion	MAGNESIUM ION
4	NMY	4	Ligand/Ion	NEOMYCIN

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NMY	1	Ligand/Ion	NEOMYCIN

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NMY	1	Ligand/Ion	NEOMYCIN

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NMY	1	Ligand/Ion	NEOMYCIN

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NMY	1	Ligand/Ion	NEOMYCIN

Asymmetric Unit (17, 17)

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 , ASP A:393 , MG A:700 , MG A:702 , HOH A:900 , HOH A:901 , HOH A:902 , HOH A:904 , HOH A:906 , HOH A:923 , HOH A:924 , HOH A:1038 , HOH A:1057 , HOH A:1093 , HOH A:1206 , HOH A:1221	binding site for residue GNP A 500
02	AC2	SOFTWARE	ASP A:374 , SER A:376 , ASP A:396 , TYR A:408 , GLU A:411 , GLU A:415 , GLU A:416 , GLU A:445 , TYR A:448 , GLU A:451 , HOH A:1151	binding site for residue NMY A 600
03	AC3	SOFTWARE	HIS A:379 , ASP A:393 , GNP A:500 , MG A:702 , HOH A:900 , HOH A:901	binding site for residue MG A 700
04	AC4	SOFTWARE	ASP A:393 , GNP A:500 , MG A:700 , HOH A:902 , HOH A:903 , HOH A:904	binding site for residue MG A 702
05	AC5	SOFTWARE	SER B:214 , ILE B:224 , LYS B:226 , TYR B:237 , TYR B:274 , GLU B:276 , ILE B:277 , PHE B:281 , HIS B:379 , ASP B:393 , MG B:700 , MG B:702 , HOH B:900 , HOH B:901 , HOH B:902 , HOH B:904 , HOH B:906 , HOH B:909 , HOH B:924 , HOH B:1154 , HOH B:1205 , HOH B:1206	binding site for residue GNP B 500
06	AC6	SOFTWARE	ASP B:374 , SER B:376 , ASP B:396 , TYR B:408 , GLU B:411 , GLU B:415 , GLU B:416 , GLU B:445 , TYR B:448 , GLU B:451 , HOH B:1250 , HOH B:1260 , HOH B:1302	binding site for residue NMY B 600
07	AC7	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
08	AC8	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
09	AC9	SOFTWARE	ASN B:199 , PHE B:200 , LYS B:201 , ASN B:220 , TYR B:223	binding site for residue GOL B 804
10	AD1	SOFTWARE	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 , ASP C:393 , MG C:700 , MG C:702 , HOH C:900 , HOH C:901 , HOH C:902 , HOH C:904 , HOH C:906 , HOH C:911 , HOH C:923 , HOH C:924 , HOH C:1038 , HOH C:1057 , HOH C:1154 , HOH C:1206 , HOH C:1221 , HOH C:1575	binding site for residue GNP C 500
11	AD2	SOFTWARE	ASN C:373 , ASP C:374 , SER C:376 , ASN C:378 , ASP C:396 , TYR C:408 , GLU C:411 , SER C:413 , GLU C:415 , GLU C:416 , GLU C:445 , TYR C:448 , GLU C:451 , HOH C:1019 , HOH C:1029 , HOH C:1047 , HOH C:1083	binding site for residue NMY C 600
12	AD3	SOFTWARE	HIS C:379 , ASP C:393 , GNP C:500 , HOH C:900 , HOH C:901	binding site for residue MG C 700
13	AD4	SOFTWARE	ASP C:393 , GNP C:500 , HOH C:902 , HOH C:903 , HOH C:904	binding site for residue MG C 702
14	AD5	SOFTWARE	SER D:214 , ILE D:224 , LYS D:226 , TYR D:274 , ILE D:277 , PHE D:281 , HIS D:379 , ASP D:393 , NMY D:600 , MG D:700 , MG D:702 , HOH D:900 , HOH D:906 , HOH D:909 , HOH D:923	binding site for residue GNP D 500
15	AD6	SOFTWARE	ASP D:374 , SER D:376 , ASP D:396 , TYR D:408 , GLU D:411 , GLU D:415 , GLU D:416 , GLU D:445 , TYR D:448 , GLU D:451 , GNP D:500 , MG D:702 , HOH D:1083 , HOH D:1119	binding site for residue NMY D 600
16	AD7	SOFTWARE	HIS D:379 , ASP D:393 , GNP D:500 , HOH D:900	binding site for residue MG D 700
17	AD8	SOFTWARE	ASP D:393 , GNP D:500 , NMY D:600 , HOH D:902 , HOH D:903	binding site for residue MG D 702

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

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

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

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

(no "Exon" information available for 5IQE)

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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeee......hhhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqe A 182 NATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   191       201       211       221       231 ||    243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473     
                                                                             233|                                                                                                                                                                                                                                                  
                                                                              236

Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               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
                 5iqe B 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   188       198       208       218       228 ||    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|                                                                                                                                                                                                                                                  
                                                                              236

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..hhhhhhhhhhhhhhhh........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
                 5iqe 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeeee..eeeeee...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
                 5iqe D 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSDSVAYLVNNEYIFKTKFSYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   188       198       208 ||    220       230|      246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476  
                                                         210|              230|                                                                                                                                                                                                                                                 
                                                          213               237

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5byl	5BYL IS SAME PROTEIN CRYSTALLIZED WITH MAGNESIUM AND GMPPCP LIGAND
5iqa
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Description

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Ligands, Modified Residues, Ions (4, 17)

Sites (17, 17)

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