4IW3 - JenaLib

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)

Title :   CRYSTAL STRUCTURE OF A PSEUDOMONAS PUTIDA PROLYL-4-HYDROXYLASE (P4H) IN COMPLEX WITH ELONGATION FACTOR TU (EF-TU)

Authors :   J. S. Scotti, M. A. Mcdonough, C. J. Schofield

Date :   23 Jan 13 (Deposition) - 29 Jan 14 (Release) - 01 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,J,K
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: J,K  (1x)

Keywords :   2-Oxoglutarate Oxygenase, Oxygen Sensing, Protein Synthesis Regulation, Double-Stranded Beta Helix, Jellyroll Fold, Prolyl-4- Hydroxylase, Translation, Metal Binding Protein-Translation Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Scotti, I. K. H. Leung, W. Ge, M. A. Bentley, J. Paps, H. B. Kramer, J. Lee, W. Aik, H. Choi, S. M. Paulsen, L. A. H. Bowman, N. D. Loik, S. Horita, C. H. Ho, N. J. Kershaw, C. M. Tang, T. D. W. Claridge, G. M. Preston, M. A. Mcdonough, C. J. Schofield
Human Oxygen Sensing May Have Origins In Prokaryotic Elongation Factor Tu Prolyl-Hydroxylation
Proc. Natl. Acad. Sci. Usa V. 111 13331 2014
PubMed-ID: 25197067 | Reference-DOI: 10.1073/PNAS.1409916111

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PP_5159
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	160488
	Strain	:	KT2440
	Synonym	:	PROLYL-4-HYDROXYLASE

Molecule 2 - ELONGATION FACTOR TU-A
	Chains	:	B, K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PP_0440, TUF-1, TUFA
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	160488
	Strain	:	KT2440
	Synonym	:	EF-TU-A

		1	2	3	4
Asymmetric Unit	:	A	B	J	K
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			J	K

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	OGA	2	Ligand/Ion	N-OXALYLGLYCINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	OGA	1	Ligand/Ion	N-OXALYLGLYCINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	OGA	1	Ligand/Ion	N-OXALYLGLYCINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:124 , ASP A:126 , HIS A:183 , OGA A:402 , HOH A:563	BINDING SITE FOR RESIDUE MN A 401
2	AC2	SOFTWARE	HIS A:124 , ASP A:126 , TYR A:141 , LEU A:154 , HIS A:183 , VAL A:185 , ARG A:192 , THR A:196 , TRP A:198 , MN A:401 , HOH A:504 , HOH A:540 , HOH A:563 , PRO B:54	BINDING SITE FOR RESIDUE OGA A 402
3	AC3	SOFTWARE	HIS B:20 , ASP B:22 , HIS B:23 , GLY B:24 , LYS B:25 , THR B:26 , THR B:27 , ASN B:136 , LYS B:137 , ASP B:139 , SER B:174 , ALA B:175 , ARG B:176 , MG B:502 , HOH B:616	BINDING SITE FOR RESIDUE GDP B 501
4	AC4	SOFTWARE	LYS B:25 , THR B:26 , CYS B:82 , GDP B:501 , HOH B:616	BINDING SITE FOR RESIDUE MG B 502
5	AC5	SOFTWARE	THR K:26 , ASP K:81 , CYS K:82 , GDP K:402 , HOH K:525 , HOH K:536 , HOH K:537	BINDING SITE FOR RESIDUE MG K 401
6	AC6	SOFTWARE	HIS K:20 , VAL K:21 , ASP K:22 , HIS K:23 , GLY K:24 , LYS K:25 , THR K:26 , THR K:27 , ASN K:136 , LYS K:137 , ASP K:139 , LEU K:140 , SER K:174 , ALA K:175 , ARG K:176 , MG K:401 , HOH K:525 , HOH K:537	BINDING SITE FOR RESIDUE GDP K 402
7	AC7	SOFTWARE	HIS J:124 , ASP J:126 , HIS J:183 , OGA J:402 , HOH J:532	BINDING SITE FOR RESIDUE MN J 401
8	AC8	SOFTWARE	TYR J:121 , HIS J:124 , ASP J:126 , VAL J:139 , TYR J:141 , LEU J:154 , HIS J:183 , VAL J:185 , ARG J:192 , THR J:196 , TRP J:198 , MN J:401 , HOH J:524 , HOH J:532 , HOH J:533 , PRO K:54	BINDING SITE FOR RESIDUE OGA J 402

(no "SS Bond" information available for 4IW3)

Asymmetric Unit

No.	Residues
1	Gly B:181	-	Lys B:182

(no "SAP(SNP)/Variant" information available for 4IW3)

(no "PROSITE Motif" information available for 4IW3)

(no "Exon" information available for 4IW3)

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:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhh....ee....hhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.....eeee.........eeeeeeee.....hhhhh..eeee.hhh.eeee......eeeee.....eee......eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iw3 A   7 HPMLAAVVDDLATHGWSQQAHFLPADLVRALAAECRRRDAEGELNPAGVGRGATQEVRETIRGDQIQWIDPGQAEACDQYLAAMDQLRLAINQGLFLGLEDFECHFALYPPGAFYRRHLDRFRDDDRRMVSAVLYLNEGWQPHDGGQLRMFLADGVEHDVEPVAGCLVVFLSGEVPHEVLPAGRERLSLTGWFRRRGNDPF 207
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain B from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4iw3b1 B:10-205 automated matches                                                                                                                                                          d4iw3b2 B:206-304 automated matches                                                                d4iw3b3 B:305-397 automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhhh...................eeeeee....eeeeee..hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhh.........eee.hhhhhhhh......hhhhhhhhhhhhhhhh....hhhhh..eee...eeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee.hhhhh.....ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iw3 B  10 LPHVNVGTIGHVDHGKTTLTAALTRVCSEVFGSKIDSAPEEKARGITINTAHVEYNSTIRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSAADGPMPQTREHILLSRQVGVPYIVVFLNKADLVAELLELVEMEVRDLLSTYDFPGDDTPIIIGSARMALEGKDDNEMGTTAVKKLVETLDSYIPEPVRAIDQPFLMPIEDVFSISGRGTVVTGRIERGIVRVQDPLEIVGLRDTTTTTCTGVEMFRKLLDEGRAGENCGVLLRGTKRDDVERGQVLVKPGSVKPHTKFTAEVYVLSKEEGGRHTPFFKGYRPQFYFRTTDVTGNCELPEGVEMVMPGDNIQMTVTLIKTIAMEDGLRFAIREGGRTVGAGVVAKIIE 397
                                    19        29        39  ||    55        65        75        85        95       105       115       125       135     ||147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
                                                           42|                                                                                         141|                                                                                                                                                                                                                                                             
                                                            49                                                                                          144

Chain J from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...ee....hhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeee.........eeeeeeee.....hhhhh..eeee.hhh.eeee......eeeee.....eee......eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iw3 J   7 HPMLAAVVDDLATHGWSQQAHFLPADLVRALAAECRRRDAEGELNPAGVGRGATQEVRETIRGDQIQWIDPGQAEACDQYLAAMDQLRLAINQGLFLGLEDFECHFALYPPGAFYRRHLDRFRDDDRRMVSAVLYLNEGWQPHDGGQLRMFLADGVEHDVEPVAGCLVVFLSGEVPHEVLPAGRERLSLTGWFRRRGNDPF 207
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain K from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4iw3k1 K:10-205 automated matches                                                                                                                                                        d4iw3k2 K:206-304 automated matches                                                                d4iw3k3 K:305-397 automated matches                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhhh.................eeeeee....eeeeee..hhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhh...eeeeeeehhhhh.hhhhhhhhhhhhhhhhh........eee.hhhhhhhh......hhhhhhhhhhhhhhhh....hhhhh..eee...eeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee..................eeee..eeeeeeee............eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iw3 K  10 LPHVNVGTIGHVDHGKTTLTAALTRVCSEVFGKIDSAPEEKAGITINTAHVEYNSTIRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSAADGPMPQTREHILLSRQVGVPYIVVFLNKADLVAELLELVEMEVRDLLSTYDFPGDDTPIIIGSARMALEGKDDNEMGTTAVKKLVETLDSYIPEPVRAIDQPFLMPIEDVFSISGRGTVVTGRIERGIVRVQDPLEIVGLRDTTTTTCTGVEMFRKLLDEGRAGENCGVLLRGTKRDDVERGQVLVKPGSVKPHTKFTAEVYVLSKEEGGRHTPFFKGYRPQFYFRTTDVTGNCELPEGVEMVMPGDNIQMTVTLIKTIAMEDGLRFAIREGGRTVGAGVVAKIIE 397
                                    19        29        39 ||     56 ||     67        77        87        97       107       117       127       137   ||  149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
                                                          41|       58|                                                                              141|                                                                                                                                                                                                                                                             
                                                           49        60                                                                               144

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 "CATH Domain" information available for 4IW3)

(no "Pfam Domain" information available for 4IW3)

Asymmetric Unit(hide GO term definitions)

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
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OGA	[ 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 ]

	Cis Peptide Bonds
		Gly B:181 - Lys B:182	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 ](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
	4iw3
		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
	EFTU1_PSEPK \| Q88QP8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q88CM1_PSEPK \| Q88CM1
		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)
	(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
	EFTU1_PSEPK \| Q88QP8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q88CM1_PSEPK \| Q88CM1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	EFTU1_PSEPK \| Q88QP8	:	4j0q
UniProtKB/TrEMBL
	Q88CM1_PSEPK \| Q88CM1	:	4j25

(no "Related Entries Specified in the PDB File" available for 4IW3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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