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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PHYTANOYL-COA DIOXYGENASE PHYHD1 (APO)

Authors :   Z. Zhang, D. Butler, M. A. Mcdonough, K. L. Kavanagh, J. E. Bray, S. S. Ng, Delft, C. H. Arrowsmith, J. Weigelt, A. Edwards, M. Sundstrom, C. J. Sc U. Oppermann, Structural Genomics Consortium (Sgc)

Date :   30 Jan 07 (Deposition) - 06 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Phyhd1, Double-Stranded Beta Helix, Oxygenase, Structural Genomics, Structural Genomics Consortium, Sgc, 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 Phytanoyl-Coa Dioxygenase Phyhd1 (Apo)
To Be Published
PubMed: search

Molecule 1 - PHYHD1 PROTEIN
	Chains	:	A
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PHYHD1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHYTANOYL-COA DIOXYGENASE DOMAIN CONTAINING 1
	Tissue	:	LUNG

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2OPW)

(no "Site" information available for 2OPW)

Asymmetric/Biological Unit

No.	Residues
1	A:3	-	A:3

Asymmetric/Biological Unit

No.	Residues
1	Gly A:104	-	His A:105
2	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 2OPW)

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 (gaps)	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
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Chain A from PDB  Type:PROTEIN  Length:286
 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-2opwA01 A:12-259                                                                                                                                                                                                                                   -------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhh....eeeee.............hhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.........eeeehhhhh..ee....eeeeeee..........eeee.........eeeee..----..eeeee.....hhhhheee......eeeee...eeee..........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 (gaps)       -----------------------------------------Exon 1.11d      Transcript 1 (2)
                 2opw A   2 ACLSPSQLQKFQQDGFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTEFSTQEEEQLRAQGSTDYFLSSGDKIRFFFEKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSFKVQTLARSLGLQMPVVVQSMYIFKQPHFGGEVSPHQDASFLYTEPLGRVLGVWIAVEDATLENGCLWFIPGSHTSGVSRRMVRAP----PGTSFLGSEPARDNSLFVPTPVQRGALVLIHGEVVHKSKQNLSDRSRQAYTFHLMEASGTTWSPENWLQPTAELPFPQLYT 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
                                                                                                                                                                                                                                      206  211

Legend:		→ Mismatch	(orange background)
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	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 2OPW)

(no "CATH Domain" information available for 2OPW)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: PhyH (5)

Homo sapiens (Human) (2)

PhyH-2opwA01

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
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	Cis Peptide Bonds
		Glu A:165 - Pro A:166	[ RasMol ]
		Gly A:104 - His A:105	[ RasMol ]

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SS Bonds (1, 1)

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Exons (11, 11)

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