Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CYSTEINE RICH INTESTINAL PROTEIN
 
Authors :  D. E. Barrick, M. Feese
Date :  19 Dec 95  (Deposition) - 11 Jul 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxygen Storage, Respiratory Protein, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Barrick
Replacement Of The Proximal Ligand Of Sperm Whale Myoglobin With Free Imidazole In The Mutant His-93-->Gly.
Biochemistry V. 33 6546 1994
PubMed-ID: 8204590  |  Reference-DOI: 10.1021/BI00187A023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYOGLOBIN (METAQUO)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: SPERM WHALE MYOGLOBIN SYNTHETIC GENE
    Expression System Plasmid: PMB413B WITH HISTIDINE 93 REPLACED WITH GLYCINE
    Expression System Taxid: 562
    Gene: SPERM WHALE MYOGLOBIN SYNTHETI
    Mutation: YES
    Organism Common: SPERM WHALE
    Organism Scientific: PHYSETER CATODON
    Organism Taxid: 9755

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD1Ligand/IonIMIDAZOLE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:42 , PHE A:43 , THR A:67 , VAL A:68 , LEU A:89 , SER A:92 , HIS A:97 , ILE A:99 , TYR A:103 , IMD A:155 , HOH A:156 , HOH A:173BINDING SITE FOR RESIDUE HEM A 154
2AC2SOFTWARELEU A:89 , SER A:92 , HIS A:97 , HEM A:154BINDING SITE FOR RESIDUE IMD A 155

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IRC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IRC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MYG_PHYCD_001 *G122AMYG_PHYCD  ---  ---AG121A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.MYG_PHYCD3-148  1A:2-147

(-) Exons   (0, 0)

(no "Exon" information available for 1IRC)

(-) 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:152
 aligned with MYG_PHYCD | P02185 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
            MYG_PHYCD     2 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQ 153
               SCOP domains d1irca_ A: Myoglobin                                                                                                                                     SCOP domains
               CATH domains 1ircA00 A:1-152 Globins                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhh.........hhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhh..hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------A------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-147 UniProt: 3-148                                                                                                               ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1irc A   1 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSGATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQ 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IRC)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYG_PHYCD | P02185)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1irc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1irc
    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
  MYG_PHYCD | P02185
    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)
  (no 'Enzyme Classificator' available)
    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
  MYG_PHYCD | P02185
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MYG_PHYCD | P02185: 101m 102m 103m 104m 105m 106m 107m 108m 109m 110m 111m 112m 1a6g 1a6k 1a6m 1a6n 1abs 1ajg 1ajh 1bvc 1bvd 1bz6 1bzp 1bzr 1ch1 1ch2 1ch3 1ch5 1ch7 1ch9 1cik 1cio 1co8 1co9 1cp0 1cp5 1cpw 1cq2 1do1 1do3 1do4 1do7 1dti 1dtm 1duk 1duo 1dxc 1dxd 1ebc 1f63 1f65 1f6h 1fcs 1h1x 1hjt 1iop 1j3f 1j52 1jdo 1jp6 1jp8 1jp9 1jpb 1jw8 1l2k 1ltw 1lue 1mbc 1mbd 1mbi 1mbn 1mbo 1mcy 1mgn 1mlf 1mlg 1mlh 1mlj 1mlk 1mll 1mlm 1mln 1mlo 1mlq 1mlr 1mls 1mlu 1moa 1mob 1moc 1mod 1mti 1mtj 1mtk 1myf 1mym 1myz 1mz0 1n9f 1n9h 1n9i 1n9x 1naz 1o16 1obm 1ofj 1ofk 1spe 1swm 1tes 1u7r 1u7s 1ufj 1ufp 1v9q 1vxa 1vxb 1vxc 1vxd 1vxe 1vxf 1vxg 1vxh 1wvp 1yog 1yoh 1yoi 2blh 2bli 2blj 2bw9 2bwh 2cmm 2d6c 2e2y 2eb8 2eb9 2ef2 2ekt 2eku 2evk 2evp 2g0r 2g0s 2g0v 2g0x 2g0z 2g10 2g11 2g12 2g14 2jho 2mb5 2mbw 2mga 2mgb 2mgc 2mgd 2mge 2mgf 2mgg 2mgh 2mgi 2mgj 2mgk 2mgl 2mgm 2mya 2myb 2myc 2myd 2mye 2oh8 2oh9 2oha 2ohb 2spl 2spm 2spn 2spo 2w6w 2w6x 2w6y 2z6s 2z6t 2zsn 2zso 2zsp 2zsq 2zsr 2zss 2zst 2zsx 2zsy 2zsz 2zt0 2zt1 2zt2 2zt3 2zt4 3a2g 3ase 3e4n 3e55 3e5i 3e5o 3ecl 3ecx 3ecz 3ed9 3eda 3edb 3h57 3h58 3k9z 3m38 3m39 3m3a 3m3b 3mn0 3nml 3o89 3ogb 3sdn 3u3e 4fwx 4fwy 4fwz 4h07 4h0b 4it8 4lpi 4mbn 4mxk 4mxl 4nxa 4nxc 4of9 4ood 4pnj 4pq6 4pqb 4pqc 4qau 4tyx 5b84 5b85 5c6y 5hav 5hlq 5hlu 5hlx 5iks 5ile 5ilm 5ilp 5ilr 5jom 5kd1 5kkk 5m3r 5m3s 5mbn 5o41

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1IRC)