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(-) Description

Title :  THE 1.58A CRYSTAL STRUCTURE OF HUMAN COPROPORPHYRINOGEN OXIDASE REVEALS THE STRUCTURAL BASIS OF HEREDITARY COPROPORPHYRIA
 
Authors :  D. S. Lee, E. Flachsova, M. Bodnarova, B. Demeler, P. Martasek, C. S. Ram
Date :  24 Jul 05  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flat Beta-Sheet Sandwiched By Helices, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. S. Lee, E. Flachsova, M. Bodnarova, B. Demeler, P. Martasek, C. S. Raman
Structural Basis Of Hereditary Coproporphyria.
Proc. Natl. Acad. Sci. Usa V. 102 14232 2005
PubMed-ID: 16176984  |  Reference-DOI: 10.1073/PNAS.0506557102

(-) Compounds

Molecule 1 - COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL
    ChainsA
    EC Number1.3.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPGEX-4T1
    Expression System Vector TypePLASMID
    FragmentCOPROPORPHYRINOGEN OXIDASE DOMAIN
    GeneCPOX, CPO, CPX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOPROPORPHYRINOGENASE, COPROGEN OXIDASE, COX

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:244 , HIS A:258 , ASN A:260 , ARG A:262 , GLY A:406 , GLY A:411 , SER A:412 , ARG A:413 , SER A:416 , HOH A:635 , HOH A:636 , HOH A:640 , HOH A:641 , HOH A:663 , HOH A:664 , HOH A:844BINDING SITE FOR RESIDUE CIT A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AEX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:344 -Pro A:345

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Asymmetric Unit (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_023444V135AHEM6_HUMANDisease (HCP)201826432AV135A
02UniProtVAR_002152G189SHEM6_HUMANDisease (HCP)759347283AG189S
03UniProtVAR_002153G197WHEM6_HUMANDisease (HCP)  ---AG197W
04UniProtVAR_002154E201KHEM6_HUMANDisease (HCP)  ---AE201K
05UniProtVAR_019067S208FHEM6_HUMANDisease (HCP)28929486AS208F
06UniProtVAR_023445L214RHEM6_HUMANDisease (HCP)  ---AL214R
07UniProtVAR_023446P249RHEM6_HUMANDisease (HCP)  ---AP249R
08UniProtVAR_002155P249SHEM6_HUMANDisease (HCP)  ---AP249S
09UniProtVAR_002156N272HHEM6_HUMANPolymorphism1131857AN272H
10UniProtVAR_058005G279RHEM6_HUMANDisease (HCP)121917874AG279R
11UniProtVAR_002157G280RHEM6_HUMANDisease (HCP)  ---AG280R
12UniProtVAR_002158V294IHEM6_HUMANPolymorphism2228056AV294I
13UniProtVAR_002159H295DHEM6_HUMANDisease (HCP)121917870AH295D
14UniProtVAR_019068R328CHEM6_HUMANDisease (HCP)28929487AR328C
15UniProtVAR_002160R331WHEM6_HUMANDisease (HCP)121917866AR331W
16UniProtVAR_048827R352CHEM6_HUMANPolymorphism11921054AR352C
17UniProtVAR_002162K404EHEM6_HUMANDisease (HCP)121917868AK404E
18UniProtVAR_002163W427RHEM6_HUMANDisease (HCP)  ---AW427R
19UniProtVAR_019069R447CHEM6_HUMANDisease (HCP)28931603AR447C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (19, 38)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_023444V135AHEM6_HUMANDisease (HCP)201826432AV135A
02UniProtVAR_002152G189SHEM6_HUMANDisease (HCP)759347283AG189S
03UniProtVAR_002153G197WHEM6_HUMANDisease (HCP)  ---AG197W
04UniProtVAR_002154E201KHEM6_HUMANDisease (HCP)  ---AE201K
05UniProtVAR_019067S208FHEM6_HUMANDisease (HCP)28929486AS208F
06UniProtVAR_023445L214RHEM6_HUMANDisease (HCP)  ---AL214R
07UniProtVAR_023446P249RHEM6_HUMANDisease (HCP)  ---AP249R
08UniProtVAR_002155P249SHEM6_HUMANDisease (HCP)  ---AP249S
09UniProtVAR_002156N272HHEM6_HUMANPolymorphism1131857AN272H
10UniProtVAR_058005G279RHEM6_HUMANDisease (HCP)121917874AG279R
11UniProtVAR_002157G280RHEM6_HUMANDisease (HCP)  ---AG280R
12UniProtVAR_002158V294IHEM6_HUMANPolymorphism2228056AV294I
13UniProtVAR_002159H295DHEM6_HUMANDisease (HCP)121917870AH295D
14UniProtVAR_019068R328CHEM6_HUMANDisease (HCP)28929487AR328C
15UniProtVAR_002160R331WHEM6_HUMANDisease (HCP)121917866AR331W
16UniProtVAR_048827R352CHEM6_HUMANPolymorphism11921054AR352C
17UniProtVAR_002162K404EHEM6_HUMANDisease (HCP)121917868AK404E
18UniProtVAR_002163W427RHEM6_HUMANDisease (HCP)  ---AW427R
19UniProtVAR_019069R447CHEM6_HUMANDisease (HCP)28931603AR447C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPROGEN_OXIDASEPS01021 Coproporphyrinogen III oxidase signature.HEM6_HUMAN316-340  1A:316-340
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPROGEN_OXIDASEPS01021 Coproporphyrinogen III oxidase signature.HEM6_HUMAN316-340  2A:316-340

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002641931aENSE00002082215chr3:98312567-98311793775HEM6_HUMAN1-1861861A:119-18668
1.2aENST000002641932aENSE00000774427chr3:98309999-98309856144HEM6_HUMAN186-234491A:186-23449
1.3aENST000002641933aENSE00000774428chr3:98309586-98309476111HEM6_HUMAN234-271381A:234-27138
1.5ENST000002641935ENSE00000774429chr3:98307698-98307557142HEM6_HUMAN271-318481A:271-31848
1.6bENST000002641936bENSE00000520584chr3:98304503-98304285219HEM6_HUMAN318-391741A:318-39174
1.7bENST000002641937bENSE00000774433chr3:98300355-98300251105HEM6_HUMAN391-426361A:391-42636
1.8ENST000002641938ENSE00000817865chr3:98299614-982982861329HEM6_HUMAN426-454291A:426-45429

(-) 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:336
 aligned with HEM6_HUMAN | P36551 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:336
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448      
           HEM6_HUMAN   119 EEDELAHRCSSFMAPPVTDLGELRRRPGDMKTKMELLILETQAQVCQALAQVDGGANFSVDRWERKEGGGGISCVLQDGCVFEKAGVSISVVHGNLSEEAAKQMRSRGKVLKTKDGKLPFCAMGVSSVIHPKNPHAPTIHFNYRYFEVEEADGNKQWWFGGGCDLTPTYLNQEDAVHFHRTLKEACDQHGPDLYPKFKKWCDDYFFIAHRGERRGIGGIFFDDLDSPSKEEVFRFVQSCARAVVPSYIPLVKKHCDDSFTPQEKLWQQLRRGRYVEFNLLYDRGTKFGLFTPGSRIESILMSLPLTARWEYMHSPSENSKEAEILEVLRHPRDWVR 454
               SCOP domains d2aexa_ A: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2aexA00 A:119-454 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeeee....eeeeeeeeeeeeee.hhhhhhhhhhh...........eeeeeeeeeeeee......eeeeeeeeeeee.....eeeeeeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhh.eeeee.........hhhhhhhhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) ----------------A-----------------------------------------------------S-------W---K------F-----R----------------------------------R----------------------H------RR-------------ID--------------------------------C--W--------------------C---------------------------------------------------E----------------------R-------------------C------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:119-186 UniProt: 1-186 [INCOMPLETE]               -----------------------------------------------Exon 1.3a  PDB: A:234-271             ----------------------------------------------Exon 1.6b  PDB: A:318-391 UniProt: 318-391                                ----------------------------------Exon 1.8  PDB: A:426-454      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.2a  PDB: A:186-234 UniProt: 186-234       ------------------------------------Exon 1.5  PDB: A:271-318 UniProt: 271-318       ------------------------------------------------------------------------Exon 1.7b  PDB: A:391-426           ---------------------------- Transcript 1 (2)
                 2aex A 119 EEDELAHRCSSFMAPPVTDLGELRRRPGDMKTKMELLILETQAQVCQALAQVDGGANFSVDRWERKEGGGGISCVLQDGCVFEKAGVSISVVHGNLSEEAAKQMRSRGKVLKTKDGKLPFCAMGVSSVIHPKNPHAPTIHFNYRYFEVEEADGNKQWWFGGGCDLTPTYLNQEDAVHFHRTLKEACDQHGPDLYPKFKKWCDDYFFIAHRGERRGIGGIFFDDLDSPSKEEVFRFVQSCARAVVPSYIPLVKKHCDDSFTPQEKLWQQLRRGRYVEFNLLYDRGTKFGLFTPGSRIESILMSLPLTARWEYMHSPSENSKEAEILEVLRHPRDWVR 454
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448      

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AEX)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (HEM6_HUMAN | P36551)
molecular function
    GO:0004109    coproporphyrinogen oxidase activity    Catalysis of the reaction: coproporphyrinogen III + 2 H(+) + O(2) = 2 CO(2) + 2 H(2)O + protoporphyrinogen IX.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005212    structural constituent of eye lens    The action of a molecule that contributes to the structural integrity of the lens of an eye.
biological process
    GO:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0006782    protoporphyrinogen IX biosynthetic process    The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
    GO:0046685    response to arsenic-containing substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0010035    response to inorganic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
    GO:0017085    response to insecticide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insecticide stimulus. Insecticides are chemicals used to kill insects.
    GO:0010039    response to iron ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
    GO:0010288    response to lead ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
    GO:0051597    response to methylmercury    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methylmercury stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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