5LBC - JenaLib

Title :   HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) I280V/R281L/I292V VARIANT IN COMPLEX WITH MN(II) AND N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL) CARBONYL]GLYCINE (IOX3/FG2216)

Authors :   R. Chowdhury, C. J. Schofield

Date :   15 Jun 16 (Deposition) - 31 Aug 16 (Release) - 07 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Non-Heme Dioxygenase, Iron, 2-Oxoglutarate, Hypoxia- Inducible Factor, Hif, Hif Prolyl Hydroxylase Domain 2, Phd2, Egln1, Oxygenase, Hypoxia, Dna-Binding, Metal-Binding, Transcription, Helix-Loop-Helix-Beta, Dsbh, Facial Triad, Cytoplasm, Transcription/Epigenetic Regulation, Signaling, Development, Cell Structure, Beta-Hydroxylation, Transcription Activator/Inhibitor, Ubl Conjugation, Polymorphism, Vitamin C, Zinc-Finger, Familial Erythrocytosis, Breast Cancer, Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Chowdhury, I. K. Leung, Y. M. Tian, M. I. Abboud, W. Ge, C. Domene, F. X. Cantrelle, I. Landrieu, A. P. Hardy, C. W. Pugh, P. J. Ratcliffe, T. D. Claridge, C. J. Schofield
Structural Basis For Oxygen Degradation Domain Selectivity Of The Hif Prolyl Hydroxylases.
Nat Commun V. 7 12673 2016
PubMed-ID: 27561929 | Reference-DOI: 10.1038/NCOMMS12673
(for further references see the PDB file header)

Compounds

Molecule 1 - EGL NINE HOMOLOG 1
	Chains	:	A
	EC Number	:	1.14.11.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A(+)
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN (181-426)
	Gene	:	EGLN1, C1ORF12, PNAS-118, PNAS-137
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	FRAGMENT: CATALYTIC DOMAIN (181-426)
	Synonym	:	HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2,HPH-2,PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2,PHD2,SM-20

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:313 , ASP A:315 , HIS A:374 , UN9 A:503 , HOH A:618	binding site for residue MN A 501
2	AC2	SOFTWARE	LYS A:204 , HIS A:205	binding site for residue CL A 502
3	AC3	SOFTWARE	ASP A:254 , ILE A:256 , MET A:299 , TYR A:303 , TYR A:310 , HIS A:313 , ASP A:315 , TYR A:329 , LEU A:343 , HIS A:374 , VAL A:376 , ARG A:383 , ARG A:398 , MN A:501 , HOH A:618 , HOH A:622	binding site for residue UN9 A 503
4	AC4	SOFTWARE	ARG A:396 , ARG A:411	binding site for residue SO4 A 504
5	AC5	SOFTWARE	ASP A:355 , ILE A:356 , GLU A:357 , LYS A:359 , ARG A:362	binding site for residue GOL A 505
6	AC6	SOFTWARE	TYR A:310 , GLU A:375 , VAL A:376 , PRO A:378 , HOH A:676	binding site for residue GOL A 506
7	AC7	SOFTWARE	LYS A:332 , ASP A:333 , PHE A:360 , HOH A:602 , HOH A:607 , HOH A:663	binding site for residue SO4 A 507
8	AC8	SOFTWARE	LYS A:262 , ARG A:312 , VAL A:314 , PRO A:373 , HOH A:604	binding site for residue BCT A 508

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
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh.......eee...hhhhhee..eeeee......hhhhhhhhhhhhhhhhhhh.......eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lbc A 188 LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLVLHCNGKLGSYKVNGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLVRVEL 414
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397      |412  
                                                                                                                                                                                                                                                  404|    
                                                                                                                                                                                                                                                   410

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (28, 28)

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
		BCT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UN9	[ 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
(no "Cis Peptide Bonds" information available for 5lbc)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5lbc
		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
	EGLN1_HUMAN \| Q9GZT9
		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)
	1.14.11.29
		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

Analysis Tools

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
	EGLN1_HUMAN \| Q9GZT9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description