4DMM - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FROM SYNECHOCOCCUS ELONGATUS PCC 7942 IN COMPLEX WITH NADP

Authors :   C. Chen, N. N. Zhuang, K. H. Lee

Date :   08 Feb 12 (Deposition) - 22 Feb 12 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.38

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

Keywords :   Rossmann Fold, Oxoacyl-Acp Reductase, Nadp Binding, Fatty Acid Biosynthsis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Chen, N. N. Zhuang, K. H. Lee
3-Oxoacyl-[Acyl-Carrier-Protein] Reductase From Synechococcus Elongatus Pcc 7942 In Complex With Nadp
To Be Published
PubMed: search

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.100
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SYNPCC7942_0684
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	1140
	Strain	:	PCC 7942

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NAP	3	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , SER A:17 , TYR A:39 , ALA A:40 , SER A:41 , SER A:42	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	GLY B:15 , SER B:17 , ARG B:18 , GLY B:19 , ILE B:20 , ASN B:38 , TYR B:39 , ALA B:40 , SER B:41 , SER B:42 , ALA B:65 , ASP B:66 , VAL B:67 , ASN B:93 , ALA B:94 , LEU B:116 , ILE B:143 , ALA B:144 , SER B:145 , TYR B:158 , LYS B:162 , PRO B:188 , GLY B:189 , PHE B:190 , ILE B:191 , THR B:193 , MET B:195 , THR B:196 , HOH B:421 , HOH B:433 , HOH B:441	BINDING SITE FOR RESIDUE NAP B 301
3	AC3	SOFTWARE	GLY C:15 , SER C:17 , ARG C:18 , GLY C:19 , ILE C:20 , ASN C:38 , TYR C:39 , ALA C:40 , SER C:41 , SER C:42 , ALA C:65 , ASP C:66 , VAL C:67 , ASN C:93 , ALA C:94 , LEU C:116 , ILE C:143 , ALA C:144 , SER C:145 , TYR C:158 , LYS C:162 , PRO C:188 , GLY C:189 , ILE C:191 , THR C:193 , HOH C:403	BINDING SITE FOR RESIDUE NAP C 301
4	AC4	SOFTWARE	GLY D:15 , SER D:17 , ARG D:18 , GLY D:19 , ILE D:20 , TYR D:39 , ALA D:40 , SER D:41 , SER D:42 , ALA D:65 , ASP D:66 , VAL D:67 , ASN D:93 , ALA D:94 , LEU D:116 , ILE D:143 , ALA D:144 , SER D:145 , TYR D:158 , LYS D:162 , PRO D:188 , GLY D:189 , PHE D:190 , ILE D:191 , THR D:193 , HOH D:409	BINDING SITE FOR RESIDUE NAP D 301

(no "SS Bond" information available for 4DMM)

Asymmetric Unit

No.	Residues
1	Leu B:204	-	Leu B:205

(no "SAP(SNP)/Variant" information available for 4DMM)

(no "PROSITE Motif" information available for 4DMM)

(no "Exon" information available for 4DMM)

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:246
 aligned with Q31QF3_SYNE7 | Q31QF3 from UniProtKB/TrEMBL  Length:249

    Alignment length:246
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
         Q31QF3_SYNE7     4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDMTSELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
               SCOP domains d4dmma_ A: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dmm A   4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDMTSELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243

Chain B from PDB  Type:PROTEIN  Length:240
 aligned with Q31QF3_SYNE7 | Q31QF3 from UniProtKB/TrEMBL  Length:249

    Alignment length:246
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
         Q31QF3_SYNE7     4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDMTSELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
               SCOP domains d4dmmb_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........------...........hhhhhhhhhhhhhhhhhhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dmm B   4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDMTS------LLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193   |     -|      213       223       233       243      
                                                                                                                                                                                                                           197    204

Chain C from PDB  Type:PROTEIN  Length:240
 aligned with Q31QF3_SYNE7 | Q31QF3 from UniProtKB/TrEMBL  Length:249

    Alignment length:246
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
         Q31QF3_SYNE7     4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDMTSELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
               SCOP domains d4dmmc_ C: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.......------.............hhhhhhhhhhhhhhhhhhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dmm C   4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDM------EKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193 |     203       213       223       233       243      
                                                                                                                                                                                                                         195    202

Chain D from PDB  Type:PROTEIN  Length:237
 aligned with Q31QF3_SYNE7 | Q31QF3 from UniProtKB/TrEMBL  Length:249

    Alignment length:246
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
         Q31QF3_SYNE7     4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIATDMTSELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
               SCOP domains d4dmmd_ D: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....---------............hhhhhhhhhhhhhhhhhhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dmm D   4 LPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEAFAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRGITVNAVAPGFIAT---------KLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVINIDGGLVMA 249
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
                                                                                                                                                                                                                       193       203

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) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Synechococcus elongatus [TaxId: 1140] (2)

1a	d4dmma_	A:
1b	d4dmmb_	B:
1c	d4dmmc_	C:
1d	d4dmmd_	D:

(no "CATH Domain" information available for 4DMM)

(no "Pfam Domain" information available for 4DMM)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q31QF3_SYNE7 | Q31QF3)

molecular function
	GO:0004316	3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity	Catalysis of the reaction: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH + H+.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu B:204 - Leu B:205	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	Q31QF3_SYNE7 \| Q31QF3	:	4dml

4dml	THE SAME PROTEIN

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (0, 0)

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