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 :  HIGH RESOLUTION CRYSTAL STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C OXIDASE
 
Authors :  J. Koepke, H. Angerer, G. Peng
Date :  04 May 09  (Deposition) - 23 Jun 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Electron Transfer, Proton Transfer, Proton Pumping, Membrane Protein, Cell Inner Membrane, Cell Membrane, Copper, Disulfide Bond, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport, Pyrrolidone Carboxylic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Koepke, E. Olkhova, H. Angerer, H. Muller, G. Peng, H. Michel
High Resolution Crystal Structure Of Paracoccus Denitrificans Cytochrome C Oxidase: New Insights Into The Active Site And The Proton Transfer Pathways
Biochim. Biophys. Acta V. 1787 635 2009
PubMed-ID: 19374884  |  Reference-DOI: 10.1016/J.BBABIO.2009.04.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C OXIDASE SUBUNIT 1-BETA
    Chains: A
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTADII
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA, CYTOCHROME AA3 SUBUNIT 1-BETA
 
Molecule 2 - CYTOCHROME C OXIDASE SUBUNIT 2
    Chains: B
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTAC, COII, CTAB
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: CYTOCHROME C OXIDASE POLYPEPTIDE II, CYTOCHROME AA3 SUBUNIT 2, OXIDASE AA(3) SUBUNIT 2
 
Molecule 3 - ANTIBODY FV FRAGMENT
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 4 - ANTIBODY FV FRAGMENT
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 32)

Asymmetric/Biological Unit (7, 32)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CU13Ligand/IonCOPPER (I) ION
3HEA2Ligand/IonHEME-A
4LDA10Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
5LMT14Ligand/IonDODECYL-BETA-D-MALTOSIDE
6MN1Ligand/IonMANGANESE (II) ION
7PEO1Ligand/IonHYDROGEN PEROXIDE

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:36 , THR A:50 , MET A:53 , ARG A:54 , TRP A:87 , ILE A:91 , HIS A:94 , MET A:98 , MET A:99 , VAL A:103 , GLY A:163 , TRP A:164 , TYR A:406 , PHE A:412 , HIS A:413 , MET A:416 , SER A:417 , ILE A:424 , MET A:452 , ILE A:459 , PHE A:460 , GLN A:463 , ARG A:473 , ARG A:474 , TYR A:475 , SER A:496 , HOH A:584 , HOH A:623BINDING SITE FOR RESIDUE HEA A 559
02AC2SOFTWARETRP A:164 , TRP A:272 , VAL A:279 , TYR A:280 , HIS A:325 , HIS A:326 , THR A:351 , GLY A:352 , GLY A:387 , GLY A:390 , LEU A:393 , SER A:394 , ASP A:399 , HIS A:403 , VAL A:408 , HIS A:411 , PHE A:412 , VAL A:415 , MET A:416 , ARG A:473 , PEO A:576 , HOH A:582 , HOH A:583 , HOH A:950 , HOH A:959 , VAL B:45 , ILE B:88BINDING SITE FOR RESIDUE HEA A 560
03AC3SOFTWAREHIS A:276 , HIS A:325 , HIS A:326 , PEO A:576BINDING SITE FOR RESIDUE CU1 A 561
04AC4SOFTWAREHIS A:403 , ASP A:404 , HOH A:578 , GLU B:218 , HOH B:285 , HOH B:884BINDING SITE FOR RESIDUE MN A 562
05AC5SOFTWAREGLU A:56 , HIS A:59 , GLY A:61 , GLN A:63 , HOH A:851 , HOH A:965BINDING SITE FOR RESIDUE CA A 563
06AC6SOFTWAREASN A:457 , PHE A:461 , LMT A:572 , LMT B:279BINDING SITE FOR RESIDUE LDA A 564
07AC7SOFTWARELEU A:72 , ILE A:73 , LDA A:567 , LMT A:571BINDING SITE FOR RESIDUE LDA A 565
08AC8SOFTWAREGLN A:336BINDING SITE FOR RESIDUE LDA A 566
09AC9SOFTWARETYR A:52 , ALA A:70 , LEU A:72 , LDA A:565BINDING SITE FOR RESIDUE LDA A 567
10BC1SOFTWARETRP A:443 , LEU A:447 , PHE A:502 , LMT A:569 , HOH A:779BINDING SITE FOR RESIDUE LMT A 568
11BC2SOFTWAREPRO A:441 , TRP A:443 , GLY A:505 , TYR A:509 , LMT A:568 , VAL D:9BINDING SITE FOR RESIDUE LMT A 569
12BC3SOFTWAREARG A:21 , LYS A:29 , LEU A:36 , MET A:435 , LEU A:511 , PRO A:537 , LMT A:575 , HOH A:964BINDING SITE FOR RESIDUE LMT A 570
13BC4SOFTWAREGLN A:58 , HIS A:59 , GLN A:63 , TYR A:64 , ALA A:74 , TYR A:494 , PHE A:497 , LDA A:565 , LMT A:572 , HOH A:593 , HOH A:771 , HOH A:787BINDING SITE FOR RESIDUE LMT A 571
14BC5SOFTWARETYR A:484 , ASN A:487 , ILE A:488 , ILE A:491 , LDA A:564 , LMT A:571 , HOH A:787 , HOH A:1306 , HOH A:1325BINDING SITE FOR RESIDUE LMT A 572
15BC6SOFTWAREILE A:367 , GLU A:368 , PHE A:369 , PHE A:377 , ASN B:61 , ARG B:62 , ARG B:63BINDING SITE FOR RESIDUE LMT A 573
16BC7SOFTWAREMET A:24 , LEU A:130 , LEU A:133BINDING SITE FOR RESIDUE LMT A 574
17BC8SOFTWARETRP A:22 , ARG A:438 , LEU A:511 , PHE A:512 , ARG A:516 , LMT A:570BINDING SITE FOR RESIDUE LMT A 575
18BC9SOFTWAREHIS A:276 , HIS A:325 , HIS A:326 , HEA A:560 , CU1 A:561BINDING SITE FOR RESIDUE PEO A 576
19CC1SOFTWARECYS B:216 , GLU B:218 , CYS B:220 , HIS B:224 , CU1 B:271BINDING SITE FOR RESIDUE CU1 B 270
20CC2SOFTWAREHIS B:181 , CYS B:216 , CYS B:220 , MET B:227 , CU1 B:270BINDING SITE FOR RESIDUE CU1 B 271
21CC3SOFTWARETHR A:389 , HIS A:464 , ASN B:19 , LDA B:274BINDING SITE FOR RESIDUE LDA B 272
22CC4SOFTWAREHIS B:36 , PHE B:37 , LDA B:276BINDING SITE FOR RESIDUE LDA B 273
23CC5SOFTWARETYR B:40 , LDA B:272 , HOH B:1291BINDING SITE FOR RESIDUE LDA B 274
24CC6SOFTWAREARG B:102 , LMT B:278 , LMT B:280BINDING SITE FOR RESIDUE LDA B 275
25CC7SOFTWAREHIS B:36 , TYR B:40 , LDA B:273BINDING SITE FOR RESIDUE LDA B 276
26CC8SOFTWAREPRO B:98 , ARG B:102 , GLU B:105 , LDA B:275BINDING SITE FOR RESIDUE LMT B 278
27CC9SOFTWAREPHE A:461 , TYR A:484 , TRP A:485 , LDA A:564 , ASN B:15 , GLY B:16 , MET B:18BINDING SITE FOR RESIDUE LMT B 279
28DC1SOFTWARETRP B:33 , LEU B:87 , ILE B:99 , LDA B:275 , HOH B:1058 , HOH B:1118 , ASN D:28BINDING SITE FOR RESIDUE LMT B 280
29DC2SOFTWARETRP A:363 , LEU B:52 , HIS B:73 , ASN B:74 , TRP B:81 , GLU B:140 , GLU B:142 , LMT B:283BINDING SITE FOR RESIDUE LMT B 281
30DC3SOFTWARELEU A:342 , THR A:346 , VAL A:349 , VAL B:86 , LEU B:89BINDING SITE FOR RESIDUE LMT B 282
31DC4SOFTWAREPHE A:356 , PHE B:48 , LEU B:51 , LEU B:52 , ILE B:55 , ILE B:80 , VAL B:84 , LMT B:281 , HOH B:1330BINDING SITE FOR RESIDUE LMT B 283

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:80
2C:22 -C:96
3D:23 -D:88

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Pro A:168 -Pro A:169
2Ser A:536 -Pro A:537
3Gln B:120 -Trp B:121
4Thr D:7 -Pro D:8
5Pro D:95 -Pro D:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HB3)

(-) PROSITE Motifs  (5, 5)

Asymmetric/Biological Unit (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1B_PARDE22-550  1A:22-545
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_PARDE41-136  1B:12-107
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_PARDE138-274  1B:109-245
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_PARDE208-256  1B:179-227
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1B_PARDE272-326  1A:272-326

(-) Exons   (0, 0)

(no "Exon" information available for 3HB3)

(-) 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:529
 aligned with COX1B_PARDE | P98002 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:529
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536         
          COX1B_PARDE    17 GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFET 545
               SCOP domains d3hb3a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hb3A00 A:17-545 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhheehhhee..........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----COX1  PDB: A:22-545 UniProt: 22-550                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: A:272-326 UniProt: 272-326              --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hb3 A  17 GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFET 545
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536         


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with COX2_PARDE | P08306 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:252
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  
           COX2_PARDE    30 QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAA 281
               SCOP domains d3hb3b1 B:1-107 Bacterial aa3 type cytochrome c oxidase subunit II                                         d3hb3b2 B:108-252 Cytochrome c oxidase                                                                                                            SCOP domains
               CATH domains 3hb3B01 B:1-24,B:106-2523hb3B02 B:25-105  [code=1.10.287.90, no name defined]                            3hb3B01 B:1-24,B:106-252 Cupredoxins -  blue copper proteins                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeee....eeeee...hhhhhhhhh.hhhhh.......eeee...eeeeeeee....eeeeehhhheeeee.....eeeeee....eeeee..............eeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -----------COX2_TM  PDB: B:12-107 UniProt: 41-136                                                          -COX2_CUA  PDB: B:109-245 UniProt: 138-274                                                                                                ------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: B:179-227 UniProt: 208-256            ------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hb3 B   1 QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAA 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with HVM54_MOUSE | P18525 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:118
                                                                                                                           117                    
                                    29        39        49        59        69        79        89        99       109       | -         -        
          HVM54_MOUSE    20 EVKLVESGGGLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVAYISNGGGSTYYPDTVKGRFTISRDNAKNNLYLQMSSLKSEDTAMYYCAR--------------------   -
               SCOP domains d3hb3c_ C: automated matches                                                                                           SCOP domains
               CATH domains 3hb3C00 C:1-118 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee........eeeeeeeee...eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3hb3 C   1 EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSS 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain D from PDB  Type:PROTEIN  Length:108
 aligned with KV5A4_MOUSE | P01636 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:108
                                                                                                                           96           
                                                                                                                         95 |           
                                    10        20        30        40        50        60        70        80        90    | | 99        
          KV5A4_MOUSE     1 DIQMTQSPDYLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYDAKTLVEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGIP-FTFGSGTKLEIK 107
               SCOP domains d3hb3d_ D: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee............eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3hb3 D   1 DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLPEDFGSYYCQHHYGTPPLTFGGGTKLEIK 108
                                    10        20        30        40        50        60        70        80        90       100
   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  (4, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HB3)

(-) Gene Ontology  (20, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COX1B_PARDE | P98002)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0004129    cytochrome-c oxidase activity    Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006119    oxidative phosphorylation    The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) 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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain B   (COX2_PARDE | P08306)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0004129    cytochrome-c oxidase activity    Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain C   (HVM54_MOUSE | P18525)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain D   (KV5A4_MOUSE | P01636)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LDA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln B:120 - Trp B:121   [ RasMol ]  
    Pro A:168 - Pro A:169   [ RasMol ]  
    Pro D:95 - Pro D:96   [ RasMol ]  
    Ser A:536 - Pro A:537   [ RasMol ]  
    Thr D:7 - Pro D:8   [ RasMol ]  
 

(-) 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
  3hb3
    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
  COX1B_PARDE | P98002
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  COX2_PARDE | P08306
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  HVM54_MOUSE | P18525
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  KV5A4_MOUSE | P01636
    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)
  1.9.3.1
    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
  COX1B_PARDE | P98002
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  COX2_PARDE | P08306
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  HVM54_MOUSE | P18525
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  KV5A4_MOUSE | P01636
    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
        COX1B_PARDE | P98002: 1ar1 1qle 1zyy 3ehb
        COX2_PARDE | P08306: 1ar1 1qle 1zyy 3ehb
        HVM54_MOUSE | P18525: 1ar1 1mqk 3ehb
        KV5A4_MOUSE | P01636: 1ar1 1mqk 3ehb

(-) Related Entries Specified in the PDB File

1ar1