3NFD - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CHRONOBACTERIUM AMMONIAGENES ACPS-COA COMPLEX

Authors :   K. Gokulan

Date :   10 Jun 10 (Deposition) - 05 Jan 11 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Acyl Carrier Protein Synthase, Mycobacterium Tuberculosis, Acyl Carrier Protein, Fatty Acid Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Gokulan, A. Aggarwal, L. Shipman, G. S. Besra, J. C. Sacchettini
Mycobacterium Tuberculosis Acyl Carrier Protein Synthase Adopts Two Different Ph-Dependent Structural Conformations.
Acta Crystallogr. , Sect. D V. 67 657 2011
PubMed-ID: 21697604 | Reference-DOI: 10.1107/S0907444911020221

Molecule 1 - PHOSPHOPANTETHEINE PROTEIN TRANSFERASE, PPT1P
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Gene	:	PPT1
	Organism Common	:	BREVIBACTERIUM AMMONIAGENES
	Organism Scientific	:	CORYNEBACTERIUM AMMONIAGENES
	Organism Taxid	:	1697

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	COA	6	Ligand/Ion	COENZYME A
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	COA	3	Ligand/Ion	COENZYME A
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	COA	3	Ligand/Ion	COENZYME A
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:65 , TRP A:108 , GLY A:109 , ARG A:110 , ILE A:136 , SER A:137 , HIS A:138 , ASP B:13 , LYS B:78 , SER B:81	BINDING SITE FOR RESIDUE COA A 154
2	AC2	SOFTWARE	HIS B:65 , ARG B:69 , GLY B:109 , VAL B:111 , ILE B:136 , SER B:137 , HIS B:138 , HOH B:276 , ASP C:13 , LYS C:78 , SER C:81 , GLN C:82	BINDING SITE FOR RESIDUE COA B 154
3	AC3	SOFTWARE	ASP A:13 , LYS A:78 , SER A:81 , GLN A:82 , HIS C:65 , ARG C:69 , GLY C:109 , VAL C:111 , ILE C:136 , SER C:137 , HIS C:138 , HOH C:422	BINDING SITE FOR RESIDUE COA C 154
4	AC4	SOFTWARE	ARG D:46 , HIS D:65 , ARG D:69 , GLY D:109 , VAL D:111 , ILE D:136 , SER D:137 , HIS D:138 , ASP E:13 , LYS E:78 , SER E:81 , GLN E:82	BINDING SITE FOR RESIDUE COA D 154
5	AC5	SOFTWARE	ARG E:47 , HIS E:65 , ARG E:69 , GLY E:109 , VAL E:111 , ILE E:136 , SER E:137 , HIS E:138 , ASP F:13 , LYS F:78 , SER F:81 , GLN F:82	BINDING SITE FOR RESIDUE COA E 154
6	AC6	SOFTWARE	ASP D:13 , LYS D:78 , SER D:81 , ARG F:46 , HIS F:65 , ARG F:69 , TRP F:108 , GLY F:109 , ARG F:110 , VAL F:111 , ILE F:136 , SER F:137 , HIS F:138	BINDING SITE FOR RESIDUE COA F 154

(no "SS Bond" information available for 3NFD)

Asymmetric Unit

No.	Residues
1	Pro A:27	-	Gly A:28
2	Ser A:61	-	Arg A:62

(no "SAP(SNP)/Variant" information available for 3NFD)

(no "PROSITE Motif" information available for 3NFD)

(no "Exon" information available for 3NFD)

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:136
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145        
         O31302_CORAM     6 EAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3nfda_ A: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhh...hhhhhh.hhhhhhhhhh.------------...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfd A   6 EAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTR------------AGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                              |     15        25        35        45|        -   |    65        75        85        95       105       115       125       135       145        
                              |                                    46           59                                                                                              
                              8-MSE

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:149
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         
         O31302_CORAM     5 REAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3nfdb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeehhhhhhhhhh..hhhhhh.hhhhhhhhhhh------------.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfd B   5 REAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTR------------AGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                               |    14        24        34        44 |       -    |   64        74        84        94       104       114       124       134       144         
                               8-MSE                                46           59

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145        
         O31302_CORAM     6 EAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3nfdc_ C: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhh....hhhhhhhhhhhhhhhh..-----------.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfd C   6 EAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRR-----------AGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                              |     15        25        35        45 |       -   |    65        75        85        95       105       115       125       135       145        
                              8-MSE                                 47          59

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145        
         O31302_CORAM     6 EAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3nfdd_ D: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhh..hhhhh..hhhhhhhhhhh--------------hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhhh..eeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfd D   6 EAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTR--------------SRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                              |     15        25        35        45|        -     |  65        75        85        95       105       115       125       135       145        
                              8-MSE                                46             61

Chain E from PDB  Type:PROTEIN  Length:139
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153
         O31302_CORAM     4 NREAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3nfde_ E: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhh.-----------...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.eeeee.....eeeeehhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nfd E   4 NREAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRR-----------AGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                                |   13        23        33        43   |     -     |  63        73        83        93       103       113       123       133       143       153
                                8-MSE                                 47          59

Chain F from PDB  Type:PROTEIN  Length:136
 aligned with O31302_CORAM | O31302 from UniProtKB/TrEMBL  Length:153

    Alignment length:148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145        
         O31302_CORAM     6 EAMTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTRRDAAADATNSSLAGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATAQCLLRYQR 153
               SCOP domains d3nfdf_ F: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---ACPS-3nfdF01 F:9-147                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) ---ACPS-3nfdF02 F:9-147                                                                                                                       ------ Pfam domains (2)
           Pfam domains (3) ---ACPS-3nfdF03 F:9-147                                                                                                                       ------ Pfam domains (3)
           Pfam domains (4) ---ACPS-3nfdF04 F:9-147                                                                                                                       ------ Pfam domains (4)
           Pfam domains (5) ---ACPS-3nfdF05 F:9-147                                                                                                                       ------ Pfam domains (5)
           Pfam domains (6) ---ACPS-3nfdF06 F:9-147                                                                                                                       ------ Pfam domains (6)
         Sec.struct. author .eeeeeeeeeehhhhhhhhh...hhhhhh.hhhhhhhhhh.------------.hhhhhhhhhhhhhhhhhhhhhhhhh............hhh.eeeee.....eeeeehhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfd F   6 EAmTVGVDLVHIPGFAEQLSRPGSTFEQVFSPLERRHAQTR------------AGSRTEHLAGRWAAKEAFIKAWSQAIYGKPPVIEPDLVNFAEIEVLPDRWGRVALQLKGEVAAKLQESIGDVELALSISHDGDYATALCLLRYQR 153
                              |     15        25        35        45|        -   |    65        75        85        95       105       115       125       135       145        
                              8-MSE                                46           59

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: 4'-phosphopantetheinyl transferase (26)

Superfamily: 4'-phosphopantetheinyl transferase (26)

Family: automated matches (19)

Protein domain: automated matches (19)

Corynebacterium ammoniagenes [TaxId: 1697] (2)

1a	d3nfda_	A:
1b	d3nfdb_	B:
1c	d3nfdc_	C:
1d	d3nfdd_	D:
1e	d3nfde_	E:
1f	d3nfdf_	F:

(no "CATH Domain" information available for 3NFD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: ACPS] (13)

Family: ACPS (13)

Corynebacterium ammoniagenes (Brevibacterium ammoniagenes) (2)

1a	ACPS-3nfdF01	F:9-147
1b	ACPS-3nfdF02	F:9-147
1c	ACPS-3nfdF03	F:9-147
1d	ACPS-3nfdF04	F:9-147
1e	ACPS-3nfdF05	F:9-147
1f	ACPS-3nfdF06	F:9-147

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (O31302_CORAM | O31302)

molecular function
	GO:0008897	holo-[acyl-carrier-protein] synthase activity	Catalysis of the reaction: CoA + substrate-serine = adenosine 3',5'-bisphosphate + substrate-serine-4'-phosphopantetheine. The transfer of the 4'-phosphopantetheine (Ppant) co-factor from coenzyme A to the hydroxyl side chain of the serine residue of acyl- or peptidyl-carrier protein (ACP or PCP) to convert them from the apo to the holo form.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Pro A:27 - Gly A:28	[ RasMol ]
		Ser A:61 - Arg A:62	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	3nfd
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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