2V4A - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SEMET-LABELED PROLYL-4 HYDROXYLASE (P4H) TYPE I FROM GREEN ALGAE CHLAMYDOMONAS REINHARDTII.

Authors :   M. K. Koski, R. Hieta, C. Bollner, K. I. Kivirikko, J. Myllyharju, R. K.

Date :   28 Jun 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Koski, R. Hieta, C. Bollner, K. I. Kivirikko, J. Myllyharju, R. K. Wierenga
The Active Site Of An Algal Prolyl 4-Hydroxylase Has A Large Structural Plasticity.
J. Biol. Chem. V. 282 37112 2007
PubMed-ID: 17940281 | Reference-DOI: 10.1074/JBC.M706554200

Molecule 1 - PROLYL-4 HYDROXYLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ORIGAMI(DE3)
	Expression System Taxid	:	562
	Organism Scientific	:	CHLAMYDOMONAS REINHARDTII
	Organism Taxid	:	3055
	Other Details	:	N-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM VAL-29 AND CONTAINING N-TERMINAL HIS-TAG
	Strain	:	CC125MT137C

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 35)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	4	Ligand/Ion	GLYCEROL
4	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:178 , LYS A:237 , HOH A:2049 , HOH A:2089	BINDING SITE FOR RESIDUE CL A1250
02	AC2	SOFTWARE	THR B:178 , LYS B:237 , HOH B:2041	BINDING SITE FOR RESIDUE CL B1250
03	AC3	SOFTWARE	THR C:178 , LYS C:237 , HOH C:2037	BINDING SITE FOR RESIDUE CL C1250
04	AC4	SOFTWARE	LEU D:166 , THR D:178 , LYS D:237	BINDING SITE FOR RESIDUE CL D1250
05	AC5	SOFTWARE	MSE B:211 , TYR B:213 , GOL B:1251 , ARG C:50 , PHE C:52	BINDING SITE FOR RESIDUE GOL C1251
06	AC6	SOFTWARE	ARG B:50 , PHE B:52 , TYR B:213 , TYR C:213 , GOL C:1251	BINDING SITE FOR RESIDUE GOL B1251
07	AC7	SOFTWARE	ARG A:50 , PHE A:52 , VAL A:118 , TYR A:213	BINDING SITE FOR RESIDUE GOL A1251
08	AC8	SOFTWARE	ARG D:50 , PHE D:52	BINDING SITE FOR RESIDUE GOL D1251
09	AC9	SOFTWARE	LYS A:110 , GLU B:61 , HOH B:2088	BINDING SITE FOR RESIDUE DMS B1252
10	BC1	SOFTWARE	GLY B:40 , LEU C:45	BINDING SITE FOR RESIDUE DMS B1253
11	BC2	SOFTWARE	ARG A:71 , HIS A:133 , HOH A:2097 , HOH A:2098 , HOH A:2099 , MSE C:74 , THR C:96 , HIS C:133 , HIS C:135	BINDING SITE FOR RESIDUE SO4 A1252

Asymmetric Unit

No.	Residues
1	A:195	-	A:230
2	B:195	-	B:230
3	C:195	-	C:230

Asymmetric Unit

No.	Residues
1	Ser A:48	-	Pro A:49
2	Ser B:48	-	Pro B:49
3	Ser C:48	-	Pro C:49
4	Ser D:48	-	Pro D:49

(no "SAP(SNP)/Variant" information available for 2V4A)

(no "PROSITE Motif" information available for 2V4A)

(no "Exon" information available for 2V4A)

Asymmetric 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:182
                                                                                                                                                                                                                      
               SCOP domains d2v4aa_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....eeee....hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee.......eeeeeeee.....ee..eee..............hhhhheee......eeeee........hhhhh.ee..eee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4a A  28 mVGFGEEWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKmVKTSTGTWFAKGEDSVISKIEKRVAQVTmIPLENHEGLQVLHYHEHGGQRVVTmLmYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALmFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPI 249
                            |   ||  40        50        60        70   | || 97       107       117  |    127       157       167       177       187       197       207   |   217       227       237       247  
                            |  32|                                    74-MSE                      120-MSE        135|      165-MSE                                       211-MSE                                  
                           28-MSE6                                      76|                                       156        167-MSE                                                                              
                                                                         94

Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee....eeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee....eeeeeeee.....ee..eee..............hhhhheee......eeeee........hhhhh.ee..eee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v4a B  28 mVGFGWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKmSTGTWFAKGEDSVISKIEKRVAQVTmIPLENHEGLQVLHYHGQRVVTmLmYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALmFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPI 249
                            |   ||  42        52        62        72 ||    102       112       122       132  ||   165 |     175       185       195       205     | 215       225       235       245    
                           28-MSE|                                  74-MSE                   120-MSE        135|     | |                                         211-MSE                                  
                                38                                   95                                      159     | |                                                                                  
                                                                                                                   165-MSE                                                                                
                                                                                                                     167-MSE

Chain C from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains d2v4ac_ C: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee....eeee....hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee....hhhhh..eeeeeeee.....ee..eee............hhhhheee......eeeee........hhhhh.ee..eee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4a C  28 mVGFGELKEEWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKmVKTSTGTWFAKGEDSVISKIEKRVAQVTmIPLENHEGLQVLHYHNAGPEHGGQRVVTmLmYLTTVEEGGETVLPNAEQKVTGWSECAKRGLAVKPIKGDALmFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPI 249
                            |       37        47        57        67      | 94       104       114     | 124       134||     160    | |170       180       192       202       212       222       232       242       
                           28-MSE                                        74-MSE                      120-MSE        135|          165-MSE                 189|                211-MSE                                  
                                                                           76|                                       152            167-MSE                192                                                         
                                                                            94

Chain D from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d2v4ad_ D: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....eeee....hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh.hhhh....eeee...eee.........hhhhh..eeeeeeee.....ee..eee............hhhhhh.eee......eeeee........hhhhheee..eee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4a D  28 mVGFGEEWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKmSTGTWFAKGEDSVISKIEKRVAQVTmIPLENHEGLQVLHYHYEPHYDYFHDPNAGPEHGGQRVVTmLmYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALmFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPI 249
                            |    || 40        50        60        70   ||  100       110       120       130    || 144     ||155       165 |     175       185       195       205     | 215       225       235       245    
                           28-MSE3|                                   74-MSE                   120-MSE        135|       150|          165-MSE                                       211-MSE                                  
                                 37                                    95                                      140        152            167-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: proly-4-hydroxylase (P4H, PHD) like (16)

Protein domain: automated matches (14)

Green alga (Chlamydomonas reinhardtii) [TaxId: 3055] (2)

1a	d2v4aa_	A:
1b	d2v4ac_	C:
1c	d2v4ad_	D:

(no "CATH Domain" information available for 2V4A)

(no "Pfam Domain" information available for 2V4A)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2V4A)

Asymmetric 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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:48 - Pro A:49	[ RasMol ]
		Ser B:48 - Pro B:49	[ RasMol ]
		Ser C:48 - Pro C:49	[ RasMol ]
		Ser D:48 - Pro D:49	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	2v4a
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

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

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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 2V4A)

2jig	CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHRDTII PROLYL-4 HYDROXYLASE TYPE I COMPLEXED WITH ZINC AND PYRIDINE-2,4-DICARBOXYLATE
2jij	CRYSTAL STRUCTURE OF THE APO FORM OF CHLAMYDOMONAS REINHARDTII PROLYL-4 HYDROXYLASE TYPE I

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 35)

Sites (11, 11)

SS Bonds (3, 3)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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