5IQC - JenaLib

Title :   AMINOGLYCOSIDE PHOSPHOTRANSFERASE (2'')-IA (CTD OF AAC(6')-IE/APH(2'')-IA) IN COMPLEX WITH GMPPNP, MAGNESIUM, AND GENTAMICIN C1

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 :   2.30

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

Compounds

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

Structural Features

Chains, Units

		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)

Ligands, Modified Residues, Ions (5, 22)

Asymmetric Unit (5, 22)

No.	Name	Count	Type	Full Name
1	51G	4	Ligand/Ion	GENTAMICIN C1
2	CL	3	Ligand/Ion	CHLORIDE ION
3	GNP	4	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4	GOL	2	Ligand/Ion	GLYCEROL
5	MG	9	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	51G	1	Ligand/Ion	GENTAMICIN C1
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4	GOL	-1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	51G	1	Ligand/Ion	GENTAMICIN C1
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	51G	1	Ligand/Ion	GENTAMICIN C1
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4	GOL	-1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	51G	1	Ligand/Ion	GENTAMICIN C1
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (22, 22)

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:208 , SER A:214 , ILE A:224 , LYS A:226 , TYR A:237 , TYR A:274 , ILE A:277 , PHE A:281 , HIS A:379 , ILE A:392 , ASP A:393 , 51G A:600 , MG A:700 , MG A:702 , HOH A:900 , HOH A:901 , HOH A:902 , HOH A:903 , HOH A:904 , HOH A:906 , HOH A:909 , HOH A:911 , HOH A:923 , HOH A:924 , HOH A:1023 , HOH A:1038 , HOH A:1091 , HOH A:1093 , HOH A:1154 , HOH A:1205 , HOH A:1206 , HOH A:1287 , HOH A:1501	binding site for residue GNP A 500
02	AC2	SOFTWARE	ASP A:374 , SER A:376 , ASP A:396 , GLU A:411 , GLU A:415 , GLU A:416 , GLU A:445 , TYR A:448 , GLU A:451 , GNP A:500 , HOH A:1029 , HOH A:1115 , HOH A:1151 , HOH A:1287	binding site for residue 51G 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	GLN A:462 , ILE A:465 , ARG A:469	binding site for residue CL A 802
06	AC6	SOFTWARE	GLY B:211 , SER B:214 , ILE B:224 , LYS B:226 , TYR B:237 , TYR B:274 , 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:903 , HOH B:904 , HOH B:906 , HOH B:909 , HOH B:911 , HOH B:924 , HOH B:925 , HOH B:1038 , HOH B:1205 , HOH B:1206 , HOH B:1299	binding site for residue GNP B 500
07	AC7	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:925 , HOH B:1151 , HOH B:1260 , HOH B:1302	binding site for residue 51G 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	ARG A:336	binding site for residue CL B 801
11	AD2	SOFTWARE	PHE B:200 , LYS B:201 , ASN B:220 , GLU B:222	binding site for residue GOL B 804
12	AD3	SOFTWARE	ILE C:208 , SER C:214 , ALA C:216 , 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:909 , HOH C:911 , HOH C:923 , HOH C:924 , HOH C:1038 , HOH C:1154 , HOH C:1206	binding site for residue GNP C 500
13	AD4	SOFTWARE	ASN C:373 , ASP C:374 , SER C:376 , ASP C:396 , TYR C:408 , GLU C:411 , GLU C:415 , GLU C:416 , GLU C:445 , GLU C:451 , HOH C:1083	binding site for residue 51G C 600
14	AD5	SOFTWARE	HIS C:379 , ASP C:393 , GNP C:500 , HOH C:900 , HOH C:901	binding site for residue MG C 700
15	AD6	SOFTWARE	ASP C:393 , GNP C:500 , HOH C:902 , HOH C:903 , HOH C:904	binding site for residue MG C 702
16	AD7	SOFTWARE	ASN C:385 , HOH C:1636 , HOH C:1637	binding site for residue MG C 800
17	AD8	SOFTWARE	GLN C:462 , ARG C:469 , HOH C:1107	binding site for residue CL C 802
18	AD9	SOFTWARE	SER D:214 , ILE D:224 , LYS D:226 , TYR D:274 , GLU D:276 , ILE D:277 , PHE D:281 , HIS D:379 , ASP D:393 , MG D:700 , MG D:702 , HOH D:900 , HOH D:902 , HOH D:903 , HOH D:906 , HOH D:909 , HOH D:925	binding site for residue GNP D 500
19	AE1	SOFTWARE	ASN D:373 , 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 , HOH D:925 , HOH D:1119	binding site for residue 51G D 600
20	AE2	SOFTWARE	HIS D:379 , ASP D:393 , GNP D:500 , HOH D:900	binding site for residue MG D 700
21	AE3	SOFTWARE	ASP D:393 , GNP D:500 , HOH D:902 , HOH D:903	binding site for residue MG D 702
22	AE4	SOFTWARE	ASN D:199 , PHE D:200 , LYS D:201	binding site for residue GOL D 804

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.......eeeeee....eeeee...eeeeeee.....hhhhhhhhhhhhhhhhh........eeeeee...eeeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqc A 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478

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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqc B 175 MEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   184       194       204       214       224     ||239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469         
                                                                                 230|                                                                                                                                                                                                                                                  
                                                                                  236

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..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqc C 183 ATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeeee..eeeee...eeeeee...hhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqc D 179 YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGDSVAYLVNNEYIFKTKFSYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTY 477
                                   188       198       208||     221       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|              230|                                                                                                                                                                                                                                                
                                                         213               237

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