4IIN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PUTATIVE 3-OXOACYL-[ACYL-CARRIER PROTEIN]REDUCTASE FROM HELICOBACTER PYLORI 26695 COMPLEXED WITH NAD+

Authors :   J. Hou, T. Osinski, H. Zheng, I. Shumilin, I. Shabalin, S. Shatsman, W. F. Anderson, W. Minor, Center For Structural Genomics Of Infe Diseases (Csgid)

Date :   20 Dec 12 (Deposition) - 09 Jan 13 (Release) - 09 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Short Chain Dehydrogenase, Fabg, Beta-Ketoacyl-Acyl Carrier Protein Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Hou, T. Osinski, H. Zheng, I. Shumilin, I. Shabalin, S. Shatsman, W. F. Anderson, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of A Putative 3-Oxoacyl-[Acyl-Carrier Protein]Reductase From Helicobacter Pylori 26695 Complexed With Nad+
To Be Published
PubMed: search

Molecule 1 - 3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE (FABG)
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.100
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HP0561, HP_0561
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	ATCC 700392 / 26695

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	K	2	Ligand/Ion	POTASSIUM ION
3	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , LYS A:15 , GLY A:16 , ILE A:17 , GLY A:18 , ASN A:35 , ARG A:37 , ASP A:63 , ALA A:64 , ASN A:90 , ALA A:91 , GLY A:92 , ASN A:113 , VAL A:140 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , ILE A:188 , THR A:190 , HOH A:403 , HOH A:442 , GLU C:52	BINDING SITE FOR RESIDUE NAD A 301
2	AC2	SOFTWARE	GLU A:237 , THR A:238 , GLU D:237 , THR D:238 , HOH D:410	BINDING SITE FOR RESIDUE K A 302
3	AC3	SOFTWARE	LYS B:15 , GLY B:16 , ILE B:17 , ASN B:35 , ARG B:37 , ASP B:63 , ALA B:64 , ASN B:90 , ALA B:91 , GLY B:92 , ASN B:113 , VAL B:140 , ALA B:141 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , ILE B:188 , ACT B:303 , HOH B:406 , HOH B:415 , HOH B:418 , HOH B:431 , HOH B:435	BINDING SITE FOR RESIDUE NAD B 301
4	AC4	SOFTWARE	GLU B:237 , THR B:238 , GLU C:237 , THR C:238 , HOH C:420	BINDING SITE FOR RESIDUE K B 302
5	AC5	SOFTWARE	SER B:142 , TYR B:155 , GLY B:186 , PHE B:187 , NAD B:301	BINDING SITE FOR RESIDUE ACT B 303
6	AC6	SOFTWARE	GLY C:12 , GLY C:16 , ILE C:17 , ASN C:35 , ARG C:37 , ASP C:63 , ALA C:64 , ASN C:90 , GLY C:92 , VAL C:93 , ASN C:113 , ALA C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , ILE C:188 , ACT C:302 , HOH C:411	BINDING SITE FOR RESIDUE NAD C 301
7	AC7	SOFTWARE	SER C:142 , TYR C:155 , PHE C:187 , NAD C:301	BINDING SITE FOR RESIDUE ACT C 302
8	AC8	SOFTWARE	GLY D:12 , LYS D:15 , GLY D:16 , ILE D:17 , ASN D:35 , ARG D:37 , ASP D:63 , ALA D:64 , ASN D:90 , GLY D:92 , VAL D:93 , ASN D:113 , VAL D:140 , ALA D:141 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , ILE D:188 , THR D:190 , ACT D:302 , HOH D:415	BINDING SITE FOR RESIDUE NAD D 301
9	AC9	SOFTWARE	SER D:142 , TYR D:155 , GLY D:186 , NAD D:301	BINDING SITE FOR RESIDUE ACT D 302

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

(no "Cis Peptide Bond" information available for 4IIN)

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

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

(no "Exon" information available for 4IIN)

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:236
                                                                                                                                                                                                                                                                            
               SCOP domains d4iina_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhh......hhhhhhhhhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iin A   0 AMQFTGKNVLITGASKGIGAEIAKTLASMGLKVWINYRSNAEVADALKNELEEKGYKAAVIKFDAASESDFIEAIQTIVQSDGGLSYLVNNAGVVRDKLAIKMKTEDFHHVIDNNLTSAFIGCREALKVMSKSRFGSVVNVASIIGERGNMGQTNYSASKGGMIAMSKSFAYEGALRNIRFNSVTPGFIETDYVKNIPLNRLGSAKEVAEAVAFLLSDHSSYITGETLKVNGGLYM 247
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189||     211       221       231       241      
                                                                                                                                                                                                                        190|                                            
                                                                                                                                                                                                                         203

Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains d4iinb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...............hhhhhhhhhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iin B   0 AMQFTGKNVLITGASKGIGAEIAKTLASMGLKVWINYRSNAEVADALKNELEEKGYKAAVIKFDAASESDFIEAIQTIVQSDGGLSYLVNNAGVVRDKLAIKMKTEDFHHVIDNNLTSAFIGCREALKVMSKSRFGSVVNVASIIGERGNMGQTNYSASKGGMIAMSKSFAYEGALRNIRFNSVTPGFIETVKNIPLNRLGSAKEVAEAVAFLLSDHSSYITGETLKVNGGLYM 247
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189||     213       223       233       243    
                                                                                                                                                                                                                        190|                                          
                                                                                                                                                                                                                         205

Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d4iinc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iin C   0 AMQFTGKNVLITGASKGIGAEIAKTLASMGLKVWINYRSNAEVADALKNELEEKGYKAAVIKFDAASESDFIEAIQTIVQSDGGLSYLVNNAGVVRDKLAIKMKTEDFHHVIDNNLTSAFIGCREALKVMSKSRFGSVVNVASIIGERGNMGQTNYSASKGGMIAMSKSFAYEGALRNIRFNSVTPGFIETKADYVKNIPLNRLGSAKEVAEAVAFLLSDHSSYITGETLKVNGGLYM 247
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189||     209       219       229       239        
                                                                                                                                                                                                                        190|                                              
                                                                                                                                                                                                                         201

Chain D from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains d4iind_ D: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhh......hhhhhhhhhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iin D   0 AMQFTGKNVLITGASKGIGAEIAKTLASMGLKVWINYRSNAEVADALKNELEEKGYKAAVIKFDAASESDFIEAIQTIVQSDGGLSYLVNNAGVVRDKLAIKMKTEDFHHVIDNNLTSAFIGCREALKVMSKSRFGSVVNVASIIGERGNMGQTNYSASKGGMIAMSKSFAYEGALRNIRFNSVTPGFIETDYVKNIPLNRLGSAKEVAEAVAFLLSDHSSYITGETLKVNGGLYM 247
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189||     211       221       231       241      
                                                                                                                                                                                                                        190|                                            
                                                                                                                                                                                                                         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/Biological 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)

Helicobacter pylori [TaxId: 85962] (12)

1a	d4iina_	A:
1b	d4iinb_	B:
1c	d4iinc_	C:
1d	d4iind_	D:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4iin)

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)

Access by PDB/NDB ID
	4iin
		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
	O25286_HELPY \| O25286
		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)
	1.1.1.100
		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

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
	O25286_HELPY \| O25286
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O25286_HELPY \| O25286	:	4ijk

4iiu
4iiv
4ij8	RELATED ID: CSGID-IDP91245 RELATED DB: TARGETTRACK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

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

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File