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(-) Description

Title :  HIF PROLYL HYDROXYLASE 2 (PHD2-R281C/V314C) CROSS-LINKED TO HIF-1ALPHA NODD-L397C/D412C AND N-OXALYLGLYCINE (NOG) (COMPLEX-2)
 
Authors :  R. Chowdhury, C. J. Schofield
Date :  14 Jun 16  (Deposition) - 31 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
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)

(-) Compounds

Molecule 1 - EGL NINE HOMOLOG 1
    Chains: A, B
    EC Number: 1.14.11.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A(+)
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2OGA2Ligand/IonN-OXALYLGLYCINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , OGA A:502 , HOH A:608binding site for residue MN A 501
2AC2SOFTWAREMET 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:608 , HOH A:611 , PRO C:402binding site for residue OGA A 502
3AC3SOFTWAREARG A:396binding site for residue SO4 A 503
4AC4SOFTWAREHIS B:313 , ASP B:315 , HIS B:374 , OGA B:502 , HOH B:606binding site for residue MN B 501
5AC5SOFTWARETYR B:310 , HIS B:313 , TYR B:329 , HIS B:374 , VAL B:376 , ARG B:383 , MN B:501 , HOH B:606 , HOH B:621 , PRO D:402binding site for residue OGA B 502

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:281 -C:412
2A:314 -C:397
3B:281 -D:412
4B:314 -D:397

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LA9)

(-) Exons   (0, 0)

(no "Exon" information available for 5LA9)

(-) Sequences/Alignments

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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhhhhh..ee........eeeee......hhhhhhhhhhhhhhhhhhh.......eeeee.eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5la9 A 188 LPALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVIRGDKITWIEGKEPGCETIGLLMSSMDDLICHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHCDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKV 401
                                   197       207       217       227       237   ||  256       266       276       286       296       306       316       326       336       346       356       366       376       386       396     
                                                                               241|                                                                                                                                                      
                                                                                251                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhh..ee..........eeeee......hhhhhhhhhhhhhhhhhhh.......eeee..eeeeeee...eeeeee........eeeeeeee.............eee........eee.....eeeeee......eeeeee..eeeeeeeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5la9 B 188 LPALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVKDIRGDKITWIEGKEPGCETIGLLMSSMDDLICHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHCDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKYLTG 406
                                   197       207       217       227       237   ||  254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404  
                                                                               241|                                                                                                                                                             
                                                                                249                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .............eee... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 5la9 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 ..............ee... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 5la9 D 395 DACTLLAPAAGDTIISLCF 413
                                   404
   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)

(no "SCOP Domain" information available for 5LA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LA9)

(-) Gene Ontology  (176, 184)

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  EGLN1_HUMAN | Q9GZT9
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  HIF1A_HUMAN | Q16665
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EGLN1_HUMAN | Q9GZT9: 2g19 2g1m 2hbt 2hbu 2y33 2y34 3hqr 3hqu 3ouh 3oui 3ouj 4bqw 4bqx 4bqy 4jzr 4kbz 4uwd 5a3u 5l9b 5l9r 5l9v 5las 5lat 5lb6 5lbb 5lbc 5lbe 5lbf 5v18
        HIF1A_HUMAN | Q16665: 1d7g 1h2k 1h2l 1h2m 1l3e 1l8c 1lm8 1lqb 2ilm 3hqr 3hqu 4ajy 4h6j 5jwp 5l9b 5l9v 5las

(-) Related Entries Specified in the PDB File

3hqr 4bqy 5l9b 5l9r 5l9v