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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROMYELOPEROXIDASE (PROMPO)
 
Authors :  I. Grishkovskaya, P. G. Furtmueller, C. Obinger, K. Djinovic-Carugo
Date :  17 Nov 16  (Deposition) - 05 Apr 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Myeloperoxidase, Prompo, Biosynthesis, Proteolytic Maturation, Halide Oxidation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Grishkovskaya, M. Paumann-Page, R. Tscheliessnig, J. Stampler, S. Hofbauer, M. Soudi, B. Sevcnikar, C. Oostenbrink, P. G. Furtmuller K. Djinovic-Carugo, W. M. Nauseef, C. Obinger
Structure Of Human Promyeloperoxidase (Prompo) And The Role Of The Propeptide In Processing And Maturation.
J. Biol. Chem. V. 292 8244 2017
PubMed-ID: 28348079  |  Reference-DOI: 10.1074/JBC.M117.775031

(-) Compounds

Molecule 1 - MYELOPEROXIDASE
    Chains: A
    EC Number: 1.11.2.2
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Gene: MPO
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MPO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 25)

Asymmetric/Biological Unit (9, 25)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3CL5Ligand/IonCHLORIDE ION
4CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6MAN2Ligand/IonALPHA-D-MANNOSE
7NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
9TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:253 , GLY A:256 , GLN A:257 , ASP A:260 , ASP A:264 , PHE A:265 , THR A:266 , ARG A:405 , GLU A:408 , MET A:409 , THR A:495 , PHE A:498 , ARG A:499 , GLY A:501 , HIS A:502 , LEU A:583 , ARG A:590 , HOH A:961 , HOH A:1010 , HOH A:1104 , HOH A:1112binding site for residue HEM A 812
02AC2SOFTWAREASP A:262 , THR A:334 , PHE A:336 , ASP A:338 , SER A:340binding site for residue CA A 813
03AC3SOFTWAREARG A:197 , TRP A:198 , ASN A:492 , VAL A:493 , TRP A:602binding site for residue CL A 814
04AC4SOFTWAREASN A:623 , HOH A:925binding site for residue CL A 815
05AC5SOFTWAREPRO A:290 , ARG A:327binding site for residue CL A 816
06AC6SOFTWAREASN A:366 , GLN A:367 , PHE A:379binding site for residue CL A 817
07AC7SOFTWAREARG A:548 , ILE A:709 , THR A:710 , HOH A:949binding site for residue CL A 818
08AC8SOFTWARELYS A:474 , ARG A:670 , MET A:688 , PEG A:822 , HOH A:1143binding site for residue PEG A 819
09AC9SOFTWAREGLN A:610 , GLN A:616 , PEG A:821 , HOH A:1144binding site for residue PEG A 820
10AD1SOFTWAREGLN A:616 , PEG A:820 , HOH A:1144binding site for residue PEG A 821
11AD2SOFTWARETYR A:475 , PHE A:605 , PEG A:819 , HOH A:1003 , HOH A:1143binding site for residue PEG A 822
12AD3SOFTWAREARG A:392 , GLU A:574 , GLN A:575 , MET A:577 , ARG A:578 , HOH A:932 , HOH A:963binding site for residue PEG A 823
13AD4SOFTWAREMET A:577 , HOH A:954 , HOH A:1107binding site for residue TRS A 824
14AD5SOFTWAREASN A:323 , PRO A:724 , PHE A:727 , VAL A:728 , ASN A:729 , HOH A:1340binding site for Mono-Saccharide NAG A 801 bound to ASN A 323
15AD6SOFTWAREASN A:355 , ASN A:358 , ALA A:364 , VAL A:365 , GLN A:367 , ARG A:368 , GLN A:370 , HOH A:905 , HOH A:978 , HOH A:1027 , HOH A:1177 , HOH A:1268 , HOH A:1318 , HOH A:1413binding site for Poly-Saccharide residues NAG A 807 through MAN A 811 bound to ASN A 355
16AD7SOFTWAREASN A:391 , TRP A:535 , LEU A:539 , HOH A:1073 , HOH A:1158 , HOH A:1365 , HOH A:1411binding site for Poly-Saccharide residues NAG A 802 through NAG A 803 bound to ASN A 391
17AD8SOFTWAREASN A:483 , SER A:485 , HOH A:1211 , HOH A:1429 , HOH A:1631binding site for Poly-Saccharide residues NAG A 804 through NAG A 805 bound to ASN A 483
18AD9SOFTWAREASN A:729 , SER A:731 , HOH A:947binding site for Mono-Saccharide NAG A 806 bound to ASN A 729

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:158 -A:319
2A:167 -A:180
3A:281 -A:291
4A:285 -A:309
5A:387 -A:398
6A:606 -A:663
7A:704 -A:730

(-) Cis Peptide Bonds  (3, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:289 -Pro A:290
2Glu A:520 -Pro A:521
3Tyr A:723 -Pro A:724

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MFA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MFA)

(-) Exons   (0, 0)

(no "Exon" information available for 5MFA)

(-) 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:588
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................................ee...............................hhhhhhhhhh..hhhhh.eeeeeehhhhhhhhhhhhhhh.....hhhhhhh.....................................................ee.......hhhhhh.hhhhhhhh................................hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh..eee.............eee.hhh..hhhhhhhh..hhhhhhhhhhheee........hhhhhh...........hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee.............eee.hhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mfa A 157 GCAYQDVGVTCPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAARASFVTGVNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRScPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREA 744
                                   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       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736        
                                                                                                                                                                                         316-CSO
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5MFA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MFA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MFA)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  PERM_HUMAN | P05164
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  1.11.2.2
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        PERM_HUMAN | P05164: 1cxp 1d2v 1d5l 1d7w 1dnu 1dnw 1mhl 1myp 3f9p 3zs0 3zs1 4c1m 4dl1 4ejx 5fiw

(-) Related Entries Specified in the PDB File

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