5L9V - JenaLib

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Title :   HIF PROLYL HYDROXYLASE 2 (PHD2-R281C/P317C) CROSS-LINKED TO HIF-1ALPHA NODD-L397C/D412C AND N-OXALYLGLYCINE (NOG) (COMPLEX-1)

Authors :   R. Chowdhury, C. J. Schofield

Date :   11 Jun 16 (Deposition) - 31 Aug 16 (Release) - 07 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

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

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)

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

Molecule 2 - HYPOXIA-INDUCIBLE FACTOR 1-ALPHA
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	N-TERMINAL OXYGEN DEPENDENT DEGRADATION DOMAIN (NODD), UNP RESIDUES 395-413
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	SYNTHETIC PEPTIDE
	Synonym	:	HIF1-ALPHA,ARNT-INTERACTING PROTEIN,BASIC-HELIX-LOOP-HELIX- PAS PROTEIN MOP1,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 78,BHLHE78, MEMBER OF PAS PROTEIN 1,PAS DOMAIN-CONTAINING PROTEIN 8
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	OGA	2	Ligand/Ion	N-OXALYLGLYCINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	OGA	1	Ligand/Ion	N-OXALYLGLYCINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	OGA	1	Ligand/Ion	N-OXALYLGLYCINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:313 , ASP A:315 , HIS A:374 , OGA A:502 , HOH A:626	binding site for residue MN A 501
2	AC2	SOFTWARE	MET A:299 , TYR A:310 , HIS A:313 , ASP A:315 , TYR A:329 , LEU A:343 , HIS A:374 , VAL A:376 , ARG A:383 , MN A:501 , HOH A:606 , HOH A:616 , HOH A:626 , HOH A:636 , PRO C:402	binding site for residue OGA A 502
3	AC3	SOFTWARE	HIS B:313 , ASP B:315 , HIS B:374 , OGA B:502 , HOH B:612	binding site for residue MN B 501
4	AC4	SOFTWARE	MET B:299 , TYR B:310 , HIS B:313 , ASP B:315 , TYR B:329 , HIS B:374 , VAL B:376 , ARG B:383 , MN B:501 , HOH B:612 , HOH B:615 , HOH B:618 , HOH B:654 , PRO D:402	binding site for residue OGA B 502

Asymmetric Unit

No.	Residues
1	A:281	-	C:412
2	A:317	-	C:397
3	B:281	-	D:412
4	B:317	-	D:397

(no "Cis Peptide Bond" information available for 5L9V)

(no "SAP(SNP)/Variant" information available for 5L9V)

(no "PROSITE Motif" information available for 5L9V)

(no "Exon" information available for 5L9V)

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
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Chain A from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...ee.................eeeee......hhhhhhhhhhhhhhhhhhh.......eeee..eeeeeee...eeeeee........eeeeeeee.....hhhhhh..eee........eee......eeeee......eeeeee..eeeeeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l9v A 189 PALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLICHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNCNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKY 403
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398

Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...ee.................eeeee......hhhhhhhhhhhhhhhhhhh.......eeee..eeeeeee...eeeeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eeeeee..eeeeeeeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l9v B 189 PALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLICHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNCNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKY 403
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398

Chain C from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhh.......ee... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 5l9v C 395 DACTLLAPAAGDTIISLCF 413
                                   404

Chain D from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhh........ee... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 5l9v D 395 DACTLLAPAAGDTIISLCF 413
                                   404

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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 5L9V)

(no "CATH Domain" information available for 5L9V)

(no "Pfam Domain" information available for 5L9V)

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