5DF1 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   IRIDOID SYNTHASE FROM CATHARANTHUS ROSEUS - TERNARY COMPLEX WITH NADP+ AND GERANIC ACID

Authors :   L. Caputi, H. Kries, C. E. M. Stevenson, M. O. Kamileen, N. H. Sherden, F. Flores, D. M. Lawson, S. E. O'Connor

Date :   26 Aug 15 (Deposition) - 28 Oct 15 (Release) - 30 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Oxidoreductase, Iridoid Synthase, Short Chain Dehydrogenase, Nadph- Dependent, Catharanthus Roseus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Kries, L. Caputi, C. E. Stevenson, M. O. Kamileen, N. H. Sherden, F. Geu-Flores, D. M. Lawson, S. E. O'Connor
Structural Determinants Of Reductive Terpene Cyclization In Iridoid Biosynthesis.
Nat. Chem. Biol. V. 12 6 2016
PubMed-ID: 26551396 | Reference-DOI: 10.1038/NCHEMBIO.1955

Molecule 1 - IRIDOID SYNTHASE
	Chains	:	A, B
	EC Number	:	1.3.1.99
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	SOLUBL21
	Expression System Vector	:	POPIN-F
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 23-388
	Organism Common	:	MADAGASCAR PERIWINKLE
	Organism Scientific	:	CATHARANTHUS ROSEUS
	Organism Taxid	:	4058
	Other Details	:	THE CRYSTALLISED PROTEIN CONTAINED RESIDUES 23-388 OF THE WILD-TYPE AMINO ACID SEQUENCE. THE SEQUENCE DIFFERED FROM DATABASE ENTRY K7WDL7 BY AN ASP TO ASN CHANGE AT POSITION 87. THE N- TERMINUS RETAINED TWO RESIDUES FROM THE NICKEL AFFINITY CLEAVAGE SITE.

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	58X	2	Ligand/Ion	(2E)-3,7-DIMETHYLOCTA-2,6-DIENOIC ACID
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	IMD	1	Ligand/Ion	IMIDAZOLE
4	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	58X	2	Ligand/Ion	(2E)-3,7-DIMETHYLOCTA-2,6-DIENOIC ACID
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	IMD	2	Ligand/Ion	IMIDAZOLE
4	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	58X	2	Ligand/Ion	(2E)-3,7-DIMETHYLOCTA-2,6-DIENOIC ACID
2	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
3	IMD	-1	Ligand/Ion	IMIDAZOLE
4	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:36 , THR A:38 , GLY A:39 , ILE A:40 , ALA A:65 , ARG A:66 , ARG A:67 , CYS A:83 , ASP A:84 , VAL A:85 , SER A:108 , TRP A:109 , MET A:121 , GLN A:142 , THR A:143 , TYR A:178 , PRO A:201 , ALA A:202 , VAL A:204 , SER A:211 , MET A:212 , MET A:213 , 58X A:901 , HOH A:1001 , HOH A:1028 , HOH A:1061 , HOH A:1075 , HOH A:1119 , HOH A:1130	binding site for residue NAP A 900
02	AC2	SOFTWARE	GLY A:144 , ILE A:145 , LYS A:146 , TYR A:178 , PHE A:342 , ALA A:346 , NAP A:900	binding site for residue 58X A 901
03	AC3	SOFTWARE	HIS A:147 , ARG A:171 , GLU A:182 , ARG A:200 , HOH A:1003 , HOH A:1007 , HOH A:1029	binding site for residue EDO A 902
04	AC4	SOFTWARE	CYS A:226 , GLU A:229 , MET A:313 , HOH A:1038 , HOH A:1137 , HOH A:1146	binding site for residue IMD A 903
05	AC5	SOFTWARE	GLY B:36 , VAL B:37 , THR B:38 , GLY B:39 , ILE B:40 , ALA B:65 , ARG B:66 , ARG B:67 , CYS B:83 , ASP B:84 , VAL B:85 , SER B:108 , TRP B:109 , MET B:121 , GLN B:142 , THR B:143 , TYR B:178 , PRO B:201 , ALA B:202 , VAL B:204 , SER B:211 , MET B:212 , MET B:213 , 58X B:901 , HOH B:1004 , HOH B:1016 , HOH B:1018 , HOH B:1020 , HOH B:1032 , HOH B:1075	binding site for residue NAP B 900
06	AC6	SOFTWARE	GLY B:144 , ILE B:145 , LYS B:146 , TYR B:178 , ALA B:346 , SER B:349 , NAP B:900	binding site for residue 58X B 901
07	AC7	SOFTWARE	HIS B:147 , ARG B:171 , GLU B:182 , ARG B:200 , HOH B:1002 , HOH B:1008 , HOH B:1009	binding site for residue EDO B 902
08	AC8	SOFTWARE	SER A:376 , SER B:86 , ASN B:87 , ASN B:88 , THR B:120 , ASN B:124 , HOH B:1027 , HOH B:1045	binding site for residue EDO B 903
09	AC9	SOFTWARE	GLU B:47 , ASP B:252 , LYS B:380 , HOH B:1001	binding site for residue EDO B 904
10	AD1	SOFTWARE	HOH B:1031 , HOH B:1122	binding site for residue EDO B 905

(no "SS Bond" information available for 5DF1)

Asymmetric Unit

No.	Residues
1	Gly A:57	-	Pro A:58
2	Ser A:163	-	Pro A:164
3	Gly B:57	-	Pro B:58
4	Ser B:163	-	Pro B:164

(no "SAP(SNP)/Variant" information available for 5DF1)

(no "PROSITE Motif" information available for 5DF1)

(no "Exon" information available for 5DF1)

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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhh.........eeeeeee....hhhhhh...eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee..hhhhhh.........................hhhhhhhhhhhhhhhhhh.eeeeeee.eee........hhhhhhhhhhhhhhhh...ee...hhhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh..ee.........hhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5df1 A  23 GVCKSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSNNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEEGSKVVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIP 388
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382

Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhh.........eeeeeee....hhhhhh...eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee..hhhhhh.........................hhhhhhhhhhhhhhhhhh.eeeeeee.eee........hhhhhhhhhhhhhhhh...ee...hhhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh..ee.........hhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5df1 B  23 GVCKSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSNNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEEGSKVVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIP 388
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382

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 '\|'

(no "SCOP Domain" information available for 5DF1)

(no "CATH Domain" information available for 5DF1)

(no "Pfam Domain" information available for 5DF1)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		58X	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gly A:57 - Pro A:58	[ RasMol ]
		Gly B:57 - Pro B:58	[ RasMol ]
		Ser A:163 - Pro A:164	[ RasMol ]
		Ser B:163 - Pro B:164	[ RasMol ]

Biological Units
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	IRIS_CATRO \| K7WDL7	:	5coa 5cob 5dbf 5dbg 5dbi 5dcu 5dcw 5dcy 5emh

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Description

Compounds

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 5)

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