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(-) Description

Title :  STRUCTURE OF CERULOPLASMIN-MYELOPEROXIDASE COMPLEX
 
Authors :  V. R. Samygina, A. V. Sokolov, G. Bourenkov, V. B. Vasilyev, H. Bartunik
Date :  07 Apr 12  (Deposition) - 10 Apr 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.69
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Cupredoxin Domains, Glycoproteins, Protein-Protein Interaction, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. R. Samygina, A. V. Sokolov, G. Bourenkov, M. V. Petoukhov, M. O. Pulina, E. T. Zakharova, V. B. Vasilyev, H. Bartunik, D. I. Svergu
Ceruloplasmin: Macromolecular Assemblies With Iron-Containing Acute Phase Proteins.
Plos One V. 8 67145 2013
PubMed-ID: 23843990  |  Reference-DOI: 10.1371/JOURNAL.PONE.0067145

(-) Compounds

Molecule 1 - CERULOPLASMIN
    Chains: A
    EC Number: 1.16.3.1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FERROXIDASE
 
Molecule 2 - MYELOPEROXIDASE LIGHT CHAIN
    Chains: B
    EC Number: 1.11.2.2
    Fragment: UNP RESIDUES 165-278
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MYELOPEROXIDASE HEAVY CHAIN
    Chains: D
    EC Number: 1.11.2.2
    Fragment: UNP RESIDUES 279-745
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CU7Ligand/IonCOPPER (II) ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:275 , HIS A:276 , CYS A:319 , ASN A:321 , HIS A:324 , LEU A:329BINDING SITE FOR RESIDUE CU A 1101
02AC2SOFTWAREHIS A:163 , HIS A:980 , LEU A:1018 , HIS A:1020BINDING SITE FOR RESIDUE CU A 1102
03AC3SOFTWAREHIS A:103 , HIS A:161 , HIS A:1022BINDING SITE FOR RESIDUE CU A 1103
04AC4SOFTWAREHIS A:101 , HIS A:103 , HIS A:978 , HIS A:980BINDING SITE FOR RESIDUE CU A 1104
05AC5SOFTWAREHIS A:637 , CYS A:680 , THR A:682 , HIS A:685 , MET A:690BINDING SITE FOR RESIDUE CU A 1105
06AC6SOFTWAREHIS A:975 , CYS A:1021 , HIS A:1026 , MET A:1031BINDING SITE FOR RESIDUE CU A 1106
07AC7SOFTWAREGLU A:272 , GLU A:935 , HIS A:940 , ASP A:1025BINDING SITE FOR RESIDUE CU A 1107
08AC8SOFTWAREASN A:119BINDING SITE FOR RESIDUE NAG A 1108
09AC9SOFTWAREASN A:378BINDING SITE FOR RESIDUE NAG A 1109
10BC1SOFTWAREMET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , GLU D:242 , MET D:243 , THR D:329 , PHE D:332 , ARG D:333 , GLY D:335 , HIS D:336 , ILE D:339 , PHE D:365 , LEU D:406 , PHE D:407 , LEU D:417 , ARG D:424BINDING SITE FOR RESIDUE HEM D 601
11BC2SOFTWAREASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201BINDING SITE FOR RESIDUE NAG D 605
12BC3SOFTWAREASN D:225 , ALA D:228 , TRP D:369BINDING SITE FOR RESIDUE NAG D 606
13BC4SOFTWARELEU B:33 , TYR D:309 , ARG D:314 , ASN D:317 , SER D:319 , VAL D:320 , ARG D:438 , PHE D:439 , GLY D:441BINDING SITE FOR LINKED RESIDUES D 602 to 604

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:155 -A:181
2A:257 -A:338
3A:515 -A:541
4A:618 -A:699
5A:855 -A:881
6B:1 -B:14
7D:115 -D:125
8D:119 -D:143
9D:221 -D:232
10D:440 -D:497
11D:538 -D:564

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Asp A:19 -His A:20
2Gly A:21 -Glu A:22
3Cys A:338 -Asn A:339
4Lys A:340 -Ser A:341
5Asp A:345 -Asn A:346
6Val A:483 -Pro A:484
7Asn A:743 -Val A:744
8Pro D:123 -Pro D:124
9Glu D:354 -Pro D:355
10Asn D:549 -Asn D:550
11Tyr D:557 -Pro D:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EJX)

(-) 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:1034
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee................hhhhh..........eeeeeeeeee.....................eee......eeeeee........ee.....hhhhh......................eee.................eeeeeee...hhhhhhh...eeeeeee....ee..ee....eeeeeeeeeee.hhhhhhhhhhhhhh.........hhhhhhh.eeeee...........eee...eeeeeeee.......eeeee....eee..eee.eeee....eeeeeee....eeeeeee.hhhhhh.....eeeee..............eeeeeeeeeeeeeee..................hhhhhhh.........eeeeeeeeee............hhhhhh......eeee..eeeeeeee.........eee............................eee..ee.............eeeeeee...hhhhhhhhh.eeeeeee................eeee.eeeee.....hhhhhhhhhh.hhhhh...hhhhhhhheeeee...........ee.....eeeeee........eeeee....eee..eee.eeee....eeeeee.....eeeeeee.hhhhhh.....eeee.................ee.eeeeeeeee....hhhhhhhhhh...................eeeeeeeee............hhhhhhhh.....eeee...eeeeeee............................eeeeeee..............eeeee......hhhhhhh..eeeeee..............eeeeeeeeee.hhh.hhhhhhhhh..hhhhh...hhhhhhh.eeeee...........eee....eeeeeee.......eeeee....eeehhhhheee.eeee....eeeeee.....eeeeeee.hhhhhhh..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ejx A    1 KEKHYYIGIIETTWDYASDHGEKKLISVDTEHSNIYLQNGPDRIGRLYKKALYLQYTDETFRTTIEKPVWLGFLGPIIKAETGDKVYVHLKNLASRPYTFHSHGITYYKEHEGAIYPDNTTDFQRADDKVYPGEQYTYMLLATEEQSPGEGDGNCVTRIYHSHIDAPKDIASGLIGPLIICKKDSLDKEKEKHIDREFVVMFSVVDENFSWYLEDNIKTYCSEPEKVDKDNEDFQQSNRMYSVNGYTFGSLSGLSMCAEDRVKWYLFGMGNEVDVHAAFFHGQALTNKNYRIDTINLFPATLFDAYMVAQNPGEWMLSCQNLNHLKAGLQAFFQVQECNKSSSKDNIRGKHVRHYYIAAEEIIWNYAPSGIDIFTKENLTAPGSDSAVFFEQGTTRIGGSYKKLVYREYTDASFTNRKERGPEEEHLGILGPVIWAEVGDTIRVTFHNKGAYPLSIEPIGVRFNKNNEGTYYSPNVPPSASHVAPTETFTYEWTVPKEVGPTNADPVCLAKMYYSAVDPTKDIFTGLIGPMKICKKGSLHANGRQKDVDKEFYLFPTVFDENESLLLEDNIRMFTTAPDQVDKEDEDFQESNKMHSMNGFMYGNQPGLTMCKGDSVVWYLFSAGNEADVHGIYFSGNTYLWRGERRDTANLFPQTSLTLHMWPDTEGTFNVECLTTDHYTGGMKQKYTVNQCRRQSEDSTFYLGERTYYIAAVEVEWDYSPQREWEKELHHLQEQNVSNAFLDKGEFYIGSKYKKVVYRQYTDSTFRVPVERKAEEEHLGILGPQLHADVGDKVKIIFKNMATRPYSIHAHGVQTESSTVTPTLPGETLTYVWKIPERSGAGTEDSACIPWAYYSTVDQVKDLYSGLIGPLIVCRRPYLKVFNPRRKLEFALLFLVFDENESWYLDDNIKTYSDHPEKVNKDDEEFIESNKMHAINGRMFGNLQGLTMHVGDEVNWYLMGMGNEIDLHTVHFHGHSFQYKHRGVYSSDVFDIFPGTYQTLEMFPRTPGIWLLHCHVTDHIHAGMETTYTVLQNE 1041
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470    || 487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    475|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     483                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:104
                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................ee...............................hhhhhhhhhh..hhhhh.eeeeeehhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                4ejx B    1 CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPA  104
                                    10        20        30        40        50        60        70        80        90       100    


Chain D from PDB  Type:PROTEIN  Length:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................................ee.......hhhhhh.hhhhhhhh................................hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh..eee.............eee.hhh..hhhhhhhh..hhhhhhhhhh.eee........hhhhhh...........hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee.............eee.hhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ejx D  113 VNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREA  578
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572
   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 4EJX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 51)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ejx
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  PERM_HUMAN | P05164
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 Related Entries

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

UniProtKB/Swiss-Prot
        CERU_HUMAN | P00450: 1kcw 2j5w 4enz
        PERM_HUMAN | P05164: 1cxp 1d2v 1d5l 1d7w 1dnu 1dnw 1mhl 1myp 3f9p 3zs0 3zs1 4c1m 4dl1 5fiw 5mfa

(-) Related Entries Specified in the PDB File

4enz