5L4L - JenaLib

Title :   POLYKETIDE KETOREDUCTASE SIMC7 - TERNARY COMPLEX WITH NADP+ AND 7-OXO-SD8

Authors :   M. Schafer, C. E. M. Stevenson, B. Wilkinson, D. M. Lawson, M. J. Buttner

Date :   25 May 16 (Deposition) - 05 Oct 16 (Release) - 05 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Short-Chain Dehydrogenase/Reductase, Ketoreductase, Simocyclinone, Dna Gyrase Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Schafer, C. E. Stevenson, B. Wilkinson, D. M. Lawson, M. J. Buttner
Substrate-Assisted Catalysis In Polyketide Reduction Proceeds Via A Phenolate Intermediate.
Cell Chem Biol V. 23 1091 2016
PubMed-ID: 27617849 | Reference-DOI: 10.1016/J.CHEMBIOL.2016.07.018

Compounds

Molecule 1 - SIMC7
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B-NB-C7
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA
	Expression System Vector Type	:	PLASMID
	Gene	:	SIMC7
	Organism Scientific	:	STREPTOMYCES ANTIBIOTICUS
	Organism Taxid	:	1890
	Other Details	:	A TWENTY RESIDUE NICKEL AFFINITY TAG WITH SEQUENCE MGSSHHHHHHSSGLVPRGSH WAS APPENDED TO THE N-TERMINUS OF THE NATIVE AMINO ACID SEQUENCE BEING DERIVED FROM THE PET-15B VECTOR CONSTRUCT NAMED PET15B-NB-C7

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	7OX	1	Ligand/Ion	7-OXO-SIMOCYCLINONE D8
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:70 , NAP A:302 , 7OX A:303 , HOH A:403 , HOH A:412 , HOH A:448	binding site for residue GOL A 301
2	AC2	SOFTWARE	GLY A:7 , GLY A:10 , SER A:11 , ILE A:12 , VAL A:31 , ARG A:32 , ALA A:48 , ASP A:49 , LEU A:50 , TYR A:69 , LEU A:93 , SER A:94 , HIS A:112 , PRO A:131 , GLU A:132 , ALA A:133 , LEU A:134 , ASN A:137 , GLU A:214 , GOL A:301 , 7OX A:303 , HOH A:403 , HOH A:430 , HOH A:431 , HOH A:435 , HOH A:448 , HOH A:452 , HOH A:499 , HOH A:500 , HOH A:505 , HOH A:543 , HOH A:557 , HOH A:568 , HOH A:614	binding site for residue NAP A 302
3	AC3	SOFTWARE	SER A:95 , ILE A:96 , TRP A:100 , PRO A:107 , ILE A:108 , MET A:111 , HIS A:112 , PRO A:131 , GLU A:132 , ALA A:133 , ASN A:137 , TYR A:229 , PRO A:230 , GLU A:232 , VAL A:233 , ILE A:237 , ARG A:244 , GOL A:301 , NAP A:302	binding site for residue 7OX A 303

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/Biological 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhhh...eeeee...........eeeee....hhhhhhhhhh...eeeee....hhhhhhhhhhhhh..eeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh.eeee.....ee...hhhhhhhhhhhhhhh.....eeeee.....eehhhhhhhhhhhhh...eeee.hhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l4l A   2 KILVTGARGSIGSRVAGKLVERGLPVRGGVRDLAAPGLPEGVEAVQADLTRPETLARALEGVDKVFLYTVPEGIAGFVDEARAAGVRHVVLLSSIAVTWPDADRDPIGRMHLAVERPIEESGLGWTFVRPEALATNALGWAPEIRGGDMVRCAYPGAYTTPVHEEDIADVVVAALTTPGHRSAAYALTGPETLTQAEQVALIGEALGRAVRCERMPEQEARAVLEGLYPAEVVDAILAGQAARDGRPAEVLDTIRAVTGRPARTFREWAGDHVAAFRP 279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		7OX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l4l)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5l4l
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	G9VYV4_STRAT \| G9VYV4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	G9VYV4_STRAT \| G9VYV4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description