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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH ZN(II)-PROTOPORPHYRIN IX
 
Authors :  M. Sugishima
Date :  26 Aug 13  (Deposition) - 27 Aug 14  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Keywords :  All Alpha, Oxygenase, Heme Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Harada, M. Sugishima, J. Harada, K. Fukuyama, K. Sugase
Distal Regulation Of Heme Binding Of Heme Oxygenase-1 Mediated By Conformational Fluctuations
Biochemistry V. 54 340 2015
PubMed-ID: 25496210  |  Reference-DOI: 10.1021/BI5009694

(-) Compounds

Molecule 1 - HEME OXYGENASE 1
    Chains: A, B, C, D, E, F, G
    EC Number: 1.14.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-232
    Gene: HMOX1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: HO-1, HSP32

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): A      
Biological Unit 2 (1x):  B     
Biological Unit 3 (1x):   C    
Biological Unit 4 (1x):    D   
Biological Unit 5 (1x):     E  
Biological Unit 6 (1x):      F 
Biological Unit 7 (1x):       G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1ZNH7Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN
Biological Unit 7 (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:18 , HIS A:25 , GLU A:29 , TYR A:134 , THR A:135 , ARG A:136 , GLY A:139 , SER A:142 , GLY A:143 , LEU A:147 , ARG A:183 , PHE A:207 , GLN B:70BINDING SITE FOR RESIDUE ZNH A 300
2AC2SOFTWAREHIS B:25 , GLU B:29 , MET B:34 , GLN B:38 , TYR B:134 , THR B:135 , ARG B:136 , GLY B:139 , SER B:142 , GLY B:143 , LEU B:147 , LYS B:179 , ARG B:183 , PHE B:207 , ASN B:210 , LYS C:69 , GLN C:70BINDING SITE FOR RESIDUE ZNH B 300
3AC3SOFTWAREHIS C:25 , GLN C:38 , THR C:135 , ARG C:136 , GLY C:139 , SER C:142BINDING SITE FOR RESIDUE ZNH C 300
4AC4SOFTWARETHR C:222 , HIS D:25 , GLU D:29 , TYR D:134 , THR D:135 , ARG D:136 , LEU D:138 , PHE D:207BINDING SITE FOR RESIDUE ZNH D 300
5AC5SOFTWAREHIS E:25 , GLU E:29 , GLN E:38 , TYR E:134 , THR E:135 , GLY E:143 , PHE E:207 , ASN E:210BINDING SITE FOR RESIDUE ZNH E 300
6AC6SOFTWAREHIS F:25 , SER F:142 , GLY F:143BINDING SITE FOR RESIDUE ZNH F 300
7AC7SOFTWAREHIS G:25BINDING SITE FOR RESIDUE ZNH G 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MEC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MEC)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec A  10 SQDLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIELFEELQALLTE 223
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec B  11 QDLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIELFEELQALLTEEH 225
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec C  11 QDLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIELFEELQALLTE 223
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhh.................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec D   9 MSQDLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIELFEELQALLTE 223
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     


Chain E from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec E  10 SQDLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIELFEELQALLTE 223
                                    19        29        39        49        59        69|       80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                      69|                                                                                                                                                        
                                                                                       71                                                                                                                                                        


Chain F from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec F  12 DLSEALKEATKEHIRAENSEFMRNFVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIEL 213
                                    21 ||     32    ||  46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
                                      23|          37|                                                                                                                                                                           
                                       25           42                                                                                                                                                                           


Chain G from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhh.......................hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mec G  12 DLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTPATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPSSGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLLNIELFEELQAL 220
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4MEC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MEC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

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  4mec
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  HMOX1_RAT | P06762
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  1.14.99.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        HMOX1_RAT | P06762: 1dve 1dvg 1irm 1ivj 1ix3 1ix4 1j02 1j2c 1ubb 1ulx 1vgi 2dy5 2e7e 2zvu 3i9t 3i9u 3wkt 4g7l 4g7p 4g7t 4g7u 4g8p 4g8u 4g8w 4g98 4g99

(-) Related Entries Specified in the PDB File

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