3OBZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF HUMAN PHYTANOYL-COA DIOXYGENASE PHYHD1 2-OXOGLUTARATE AND IRON COMPLEX

Authors :   Z. Zhang, M. A. Mcdonough, C. J. Schofield

Date :   09 Aug 10 (Deposition) - 01 Sep 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Double Stranded Beta Helix Fold, Oxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, D. Butler, M. A. Mcdonough, K. L. Kavanagh, J. E. Bray, S. S. Ng F. Von Delft, C. H. Arrowsmith, J. Weigelt, A. Edwards, M. Sundstrom, C. J. Schofield, U. Oppermann
Crystal Structure Of Human Phyhd1, A Non-Heme Fe(Ii) And 2-Oxoglutarate Dependent Oxygenase Related To Phytanoyl-Coa Hydroxylase
To Be Published
PubMed: search

Molecule 1 - PHYTANOYL-COA DIOXYGENASE DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PHYHD1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHYHD1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	FE2	1	Ligand/Ion	FE (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:143 , LYS A:145 , HIS A:156 , ASP A:158 , TRP A:174 , LEU A:187 , HIS A:246 , SER A:248 , ARG A:257 , THR A:261 , HOH A:466 , FE2 A:482	BINDING SITE FOR RESIDUE AKG A 481
2	AC2	SOFTWARE	HIS A:156 , ASP A:158 , HIS A:246 , HOH A:466 , AKG A:481	BINDING SITE FOR RESIDUE FE2 A 482

(no "SS Bond" information available for 3OBZ)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:165	-	Pro A:166

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_050529	R	222	W	PHYD1_HUMAN	Polymorphism	10988159	A	R	222	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3OBZ)

Asymmetric/Biological Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000372592	1a	ENSE00001404383	chr9:131683174-131683947	774	PHYD1_HUMAN	-	0	0	-	-
1.2b	ENST00000372592	2b	ENSE00001426496	chr9:131684209-131684326	118	PHYD1_HUMAN	-	0	0	-	-
1.3a	ENST00000372592	3a	ENSE00001412360	chr9:131684562-131684635	74	PHYD1_HUMAN	1-11	11	1	A:2-11	10
1.4b	ENST00000372592	4b	ENSE00002172845	chr9:131689317-131689475	159	PHYD1_HUMAN	12-64	53	1	A:12-64	53
1.5c	ENST00000372592	5c	ENSE00001622652	chr9:131696061-131696136	76	PHYD1_HUMAN	65-90	26	1	A:65-90	26
1.6a	ENST00000372592	6a	ENSE00001653906	chr9:131696290-131696337	48	PHYD1_HUMAN	90-106	17	1	A:90-106	17
1.7	ENST00000372592	7	ENSE00001591889	chr9:131698727-131698782	56	PHYD1_HUMAN	106-124	19	1	A:106-124	19
1.8	ENST00000372592	8	ENSE00001744807	chr9:131698862-131698924	63	PHYD1_HUMAN	125-145	21	1	A:125-145	21
1.9b	ENST00000372592	9b	ENSE00001673454	chr9:131700036-131700057	22	PHYD1_HUMAN	146-153	8	1	A:146-153	8
1.10b	ENST00000372592	10b	ENSE00001757060	chr9:131702648-131702776	129	PHYD1_HUMAN	153-196	44	1	A:153-196	44
1.10e	ENST00000372592	10e	ENSE00001619664	chr9:131702878-131702994	117	PHYD1_HUMAN	196-235	40	1	A:196-235	40
1.11a	ENST00000372592	11a	ENSE00001776873	chr9:131703724-131703850	127	PHYD1_HUMAN	235-277	43	1	A:235-277	43
1.11d	ENST00000372592	11d	ENSE00001853182	chr9:131703947-131704316	370	PHYD1_HUMAN	277-291	15	1	A:277-291	15

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:290
 aligned with PHYD1_HUMAN | Q5SRE7 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:290
                                    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       281       291
          PHYD1_HUMAN     2 ACLSPSQLQKFQQDGFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTEFSTQEEEQLRAQGSTDYFLSSGDKIRFFFEKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSFKVQTLARSLGLQMPVVVQSMYIFKQPHFGGEVSPHQDASFLYTEPLGRVLGVWIAVEDATLENGCLWFIPGSHTSGVSRRMVRAPVGSAPGTSFLGSEPARDNSLFVPTPVQRGALVLIHGEVVHKSKQNLSDRSRQAYTFHLMEASGTTWSPENWLQPTAELPFPQLYT 291
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------PhyH-3obzA01 A:12-259                                                                                                                                                                                                                                   -------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhh....eeeee.hhhh........hhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.........eeeehhhhh..ee....eeeeeee..........eee..........eeeee........eeeee.....hhhhheee......eeeee....eee..........eeeeeeee....ee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a Exon 1.4b  PDB: A:12-64 UniProt: 12-64               Exon 1.5c  PDB: A:65-90   ---------------Exon 1.7           Exon 1.8             -------Exon 1.10b  PDB: A:153-196 UniProt: 153-196 --------------------------------------Exon 1.11a  PDB: A:235-277 UniProt: 235-277-------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.6a        ---------------------------------------1.9b    ------------------------------------------Exon 1.10e  PDB: A:196-235              -----------------------------------------Exon 1.11d      Transcript 1 (2)
                 3obz A   2 ACLSPSQLQKFQQDGFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTEFSTQEEEQLRAQGSTDYFLSSGDKIRFFFEKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSFKVQTLARSLGLQMPVVVQSMYIFKQPHFGGEVSPHQDASFLYTEPLGRVLGVWIAVEDATLENGCLWFIPGSHTSGVSRRMVRAPVGSAPGTSFLGSEPARDNSLFVPTPVQRGALVLIHGEVVHKSKQNLSDRSRQAYTFHLMEASGTTWSPENWLQPTAELPFPQLYT 291
                                    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       281       291

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 3OBZ)

(no "CATH Domain" information available for 3OBZ)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: PhyH (5)

Homo sapiens (Human) (2)

PhyH-3obzA01

A:12-259

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PHYD1_HUMAN | Q5SRE7)

molecular function
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	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/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
		AKG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Glu A:165 - Pro A:166	[ RasMol ]

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
	3obz
		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
	PHYD1_HUMAN \| Q5SRE7
		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)
	1.-.-.-
		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
	PHYD1_HUMAN \| Q5SRE7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PHYD1_HUMAN \| Q5SRE7	:	2opw

(no "Related Entries Specified in the PDB File" available for 3OBZ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (11, 11)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (5, 5)

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