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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE AT 1.7 ANGSTROMS RESOLUTION
 
Authors :  L. Bonnefond, J. Cavarelli
Date :  02 Oct 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Oxidoreductase, Heme-Dependent Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bonnefond, J. Cavarelli
Crystal Structure Of Human Myeloperoxidase At 1. 7 Angstroms Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MYELOPEROXIDASE
    Cell: NEUTROPHILS
    Chains: A, B
    EC Number: 1.11.2.2
    Fragment: UNP RESIDUES 167-271
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MPO
 
Molecule 2 - MYELOPEROXIDASE
    Cell: NEUTROPHILS
    Chains: C, D
    EC Number: 1.11.2.2
    Fragment: UNP RESIDUES 279-744
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MPO

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 27)

Asymmetric Unit (8, 27)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3CL5Ligand/IonCHLORIDE ION
4CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
5FUC2Ligand/IonALPHA-L-FUCOSE
6HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7MAN2Ligand/IonALPHA-D-MANNOSE
8NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (6, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
5FUC1Ligand/IonALPHA-L-FUCOSE
6HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7MAN1Ligand/IonALPHA-D-MANNOSE
8NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (6, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
5FUC1Ligand/IonALPHA-L-FUCOSE
6HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7MAN1Ligand/IonALPHA-D-MANNOSE
8NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:32 , ASN C:326 , VAL C:327BINDING SITE FOR RESIDUE CL A 602
02AC2SOFTWAREMET A:87 , GLY A:90 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , HOH A:2125 , HOH A:2127 , HOH A:2128 , ARG C:239 , GLU C:242 , MET C:243 , THR C:329 , PHE C:332 , ARG C:333 , GLY C:335 , HIS C:336 , PHE C:365 , LEU C:417 , ARG C:424BINDING SITE FOR RESIDUE HEM A 605
03AC3SOFTWAREMET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , HOH B:2107 , HOH B:2116 , HOH B:2117 , ARG D:239 , GLU D:242 , MET D:243 , THR D:329 , PHE D:332 , ARG D:333 , GLY D:335 , HIS D:336 , PHE D:365 , LEU D:417 , ARG D:424BINDING SITE FOR RESIDUE HEM B 605
04AC4SOFTWARETRP B:32 , ASN D:326 , VAL D:327 , TRP D:436BINDING SITE FOR RESIDUE CL B 201
05AC5SOFTWAREASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174BINDING SITE FOR RESIDUE CA C 601
06AC6SOFTWARETRP B:32 , BMA C:642 , HOH C:2323 , HOH C:2330 , HOH C:2331 , HOH C:2332 , PHE D:439 , LYS D:505 , FUC D:645BINDING SITE FOR RESIDUE BMA C 644
07AC7SOFTWAREARG C:382 , THR C:544 , HOH C:2195BINDING SITE FOR RESIDUE CL C 611
08AC8SOFTWAREGLN C:201 , PHE C:213BINDING SITE FOR RESIDUE CL C 612
09AC9SOFTWAREASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174BINDING SITE FOR RESIDUE CA D 701
10BC1SOFTWARETRP A:32 , PHE C:439 , LYS C:505 , FUC C:645 , HOH C:2279 , HOH C:2333 , HOH C:2334 , BMA D:642 , HOH D:2342BINDING SITE FOR RESIDUE BMA D 644
11BC2SOFTWAREGLN D:201 , PHE D:213BINDING SITE FOR RESIDUE CL D 612
12BC3SOFTWAREASN C:189 , ASN C:192 , LEU C:196 , ALA C:198 , VAL C:199 , GLN C:201 , HOH C:2080 , HOH C:2081 , HOH C:2318 , HOH C:2319BINDING SITE FOR MONO-SACCHARIDE NAG C 620 BOUND TO ASN C 189
13BC4SOFTWAREASN C:225 , TRP C:369 , LEU C:373BINDING SITE FOR MONO-SACCHARIDE NAG C 630 BOUND TO ASN C 225
14BC5SOFTWARELEU B:33 , ASN C:317 , SER C:319 , VAL C:320 , ARG C:504 , BMA C:644 , HOH C:2169 , HOH C:2278 , HOH C:2320 , HOH C:2322 , HOH C:2323 , HOH C:2324 , HOH C:2325 , HOH C:2326 , HOH C:2328 , HOH C:2329 , HOH C:2333 , HOH C:2334 , LYS D:308 , ARG D:438 , PHE D:439 , GLY D:441 , BMA D:644BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG C 640 THROUGH FUC C 645 BOUND TO ASN C 317
15BC6SOFTWAREASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201 , HOH D:2085 , HOH D:2086 , HOH D:2338BINDING SITE FOR MONO-SACCHARIDE NAG D 620 BOUND TO ASN D 189
16BC7SOFTWAREASN D:225 , TRP D:369BINDING SITE FOR MONO-SACCHARIDE NAG D 630 BOUND TO ASN D 225
17BC8SOFTWARELEU A:33 , LYS C:308 , ARG C:438 , PHE C:439 , GLY C:441 , BMA C:644 , HOH C:2159 , HOH C:2240 , HOH C:2241 , HOH C:2243 , HOH C:2277 , HOH C:2331 , HOH C:2332 , ASN D:317 , SER D:319 , VAL D:320 , BMA D:644 , HOH D:2189 , HOH D:2198 , HOH D:2339 , HOH D:2340 , HOH D:2341 , HOH D:2343 , HOH D:2344BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG D 640 THROUGH FUC D 645 BOUND TO ASN D 317

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:1 -A:14
2B:1 -B:14
3C:115 -C:125
4C:119 -C:143
5C:153 -D:153
6C:221 -C:232
7C:440 -C:497
8C:538 -C:564
9D:115 -D:125
10D:119 -D:143
11D:221 -D:232
12D:538 -D:564

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Pro C:123 -Pro C:124
2Glu C:354 -Pro C:355
3Asn C:549 -Asn C:550
4Tyr C:557 -Pro C:558
5Pro D:123 -Pro D:124
6Glu D:354 -Pro D:355
7Asn D:549 -Asn D:550
8Tyr D:557 -Pro D:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FIW)

(-) 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:105
                                                                                                                                         
               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
                 5fiw A   1 CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAA 105
                                    10        20        30        40        50        60        70        80        90       100     


Chain B from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               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
                 5fiw B   1 CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEP 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain C from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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
                 5fiw C 114 NCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRScPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWRE 577
                                   123       133       143      |153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573    
                                                              150-CSO                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................ee.......hhhhhh.hhhhhhhh...............................hhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh..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
                 5fiw D 114 NCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRScPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWRE 577
                                   123       133       143      |153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573    
                                                              150-CSO
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  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 5FIW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

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 Related Entries

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UniProtKB/Swiss-Prot
        PERM_HUMAN | P05164: 1cxp 1d2v 1d5l 1d7w 1dnu 1dnw 1mhl 1myp 3f9p 3zs0 3zs1 4c1m 4dl1 4ejx 5mfa

(-) Related Entries Specified in the PDB File

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