2OC5 - JenaLib

Title :   CRYSTAL STRUCTURE OF A FERRITIN-LIKE PROTEIN (PMT1231) FROM PROCHLOROCOCCUS MARINUS STR. MIT 9313 AT 1.68 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   20 Dec 06 (Deposition) - 13 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

Chains :   Asym./Biol. Unit : A

Keywords :   Duf3066 Family Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Np_895059. 1) Fro Prochlorococcus Marinus Mit9313 At 1. 68 A Resolution
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:45 , GLU A:73 , HIS A:76 , GLU A:157 , FE A:302 , UNL A:304 , HOH A:322 , HOH A:329	BINDING SITE FOR RESIDUE FE A 301
2	AC2	SOFTWARE	GLU A:73 , GLU A:128 , HIS A:160 , FE A:301 , UNL A:304 , HOH A:322	BINDING SITE FOR RESIDUE FE A 302
3	AC3	SOFTWARE	GLU A:47 , ASN A:51 , PHE A:100 , PHE A:107 , ILE A:127 , HOH A:328 , HOH A:373	BINDING SITE FOR RESIDUE ACT A 303
4	AC4	SOFTWARE	TYR A:34 , ILE A:37 , ASN A:38 , GLU A:45 , ALA A:48 , GLU A:73 , GLN A:123 , ILE A:127 , GLU A:128 , TYR A:138 , FE A:301 , FE A:302 , HOH A:329	BINDING SITE FOR RESIDUE UNL A 304

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:222
 aligned with ALDEC_PROMM | Q7V6D4 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:222
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239  
          ALDEC_PROMM    20 EALPDFTSDRYKDAYSRINAIVIEGEQEAHDNYIAIGTLLPDHVEELKRLAKMEMRHKKGFTACGKNLGVEADMDFAREFFAPLRDNFQTALGQGKTPTCLLIQALLIEAFAISAYHTYIPVSDPFARKITEGVVKDEYTHLNYGEAWLKANLESCREELLEANRENLPLIRRMLDQVAGDAAVLQMDKEDLIEDFLIAYQESLTEIGFNTREITRMAAAAL 241
               SCOP domains d2oc5a1 A:20-241 Hypothetical protein PMT1231                                                                                                                                                                                  SCOP domains
               CATH domains -------2oc5A01 A:27-241  [code=1.20.1260.10, no name defined]                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oc5 A  20 EALPDFTSDRYKDAYSRINAIVIEGEQEAHDNYIAIGTLLPDHVEELKRLAKmEmRHKKGFTACGKNLGVEADmDFAREFFAPLRDNFQTALGQGKTPTCLLIQALLIEAFAISAYHTYIPVSDPFARKITEGVVKDEYTHLNYGEAWLKANLESCREELLEANRENLPLIRRmLDQVAGDAAVLQmDKEDLIEDFLIAYQESLTEIGFNTREITRmAAAAL 241
                                    29        39        49        59        69  | |   79        89   |    99       109       119       129       139       149       159       169       179       189   |   199      |209       219       229      |239  
                                                                               72-MSE               93-MSE                                                                                             193-MSE      206-MSE                       236-MSE 
                                                                                 74-MSE

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ALDEC_PROMM | Q7V6D4)


GO:0071771	aldehyde decarbonylase activity	Catalysis of the reaction: a C(n) aldehyde = C(n-1) alkane + CO.
GO:1990465	aldehyde oxygenase (deformylating) activity	Catalysis of the reaction a long-chain aldehyde + O(2) + 2 NADPH = an alkane + formate + H(2)O + 2 NADP(+).
GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
GO:0009924	octadecanal decarbonylase activity	Catalysis of the reaction: octadecanal = heptadecane + CO.
GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oc5)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2oc5
		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
	ALDEC_PROMM \| Q7V6D4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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

Description