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(-) Description

Title :  STRUCTURE OF BOVINE LACTOPEROXIDASE WITH A PARTIALLY MODIFIED COVALENT BOND WITH HEME MOIETY
 
Authors :  P. Tiwari, P. K. Singh, H. V. Sirohi, P. Kaur, S. Sharma, T. P. Singh
Date :  12 Jul 16  (Deposition) - 27 Jul 16  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Singh, H. V. Sirohi, N. Iqbal, P. Tiwari, P. Kaur, S. Sharma, T. P. Singh
Structure Of Bovine Lactoperoxidase With A Partially Linked Heme Moiety At 1. 98 Angstrom Resolution
Biochim. Biophys. Acta V. 1865 329 2016
PubMed-ID: 27986533  |  Reference-DOI: 10.1016/J.BBAPAP.2016.12.006

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: LPO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 30)

Asymmetric/Biological Unit (8, 30)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IOD18Ligand/IonIODIDE ION
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6OSM2Ligand/Ion1-(OXIDOSULFANYL)METHANAMINE
7SCN1Ligand/IonTHIOCYANATE ION
8SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190binding site for residue CA A 706
02AC2SOFTWAREMET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , ARG A:255 , GLU A:258 , GLN A:259 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , LEU A:417 , LEU A:433 , ILE A:436 , ARG A:440 , IOD A:709 , HOH A:811 , HOH A:814 , HOH A:892binding site for residue HEM A 707
03AC3SOFTWAREARG A:96 , NAG A:701 , HOH A:881binding site for residue SCN A 708
04AC4SOFTWAREGLN A:105 , HIS A:109 , GLU A:258 , HEM A:707 , HOH A:801binding site for residue IOD A 709
05AC5SOFTWARETRP A:530 , IOD A:711binding site for residue IOD A 710
06AC6SOFTWAREIOD A:710binding site for residue IOD A 711
07AC7SOFTWARETRP A:46 , VAL A:342binding site for residue IOD A 712
08AC8SOFTWAREIOD A:714 , HOH A:860 , HOH A:1138binding site for residue IOD A 713
09AC9SOFTWAREASN A:80 , PRO A:145 , IOD A:713binding site for residue IOD A 714
10AD1SOFTWARETRP A:46 , VAL A:342binding site for residue IOD A 715
11AD2SOFTWAREARG A:31 , IOD A:720 , HOH A:926binding site for residue IOD A 716
12AD3SOFTWARETHR A:66binding site for residue IOD A 717
13AD4SOFTWAREPRO A:197binding site for residue IOD A 718
14AD5SOFTWARESER A:359 , HOH A:937binding site for residue IOD A 719
15AD6SOFTWARETYR A:331 , IOD A:716 , HOH A:1120binding site for residue IOD A 720
16AD7SOFTWARELYS A:462 , THR A:463 , IOD A:722binding site for residue IOD A 721
17AD8SOFTWAREIOD A:721 , HOH A:1123binding site for residue IOD A 722
18AD9SOFTWAREHIS A:377binding site for residue IOD A 723
19AE1SOFTWAREPRO A:236 , IOD A:725binding site for residue IOD A 724
20AE2SOFTWARETHR A:425 , IOD A:724binding site for residue IOD A 725
21AE3SOFTWAREASN A:419binding site for residue IOD A 726
22AE4SOFTWAREGLU A:363 , TYR A:365 , ARG A:397 , HIS A:558 , ILE A:559 , THR A:560 , LYS A:561binding site for residue OSM A 727
23AE5SOFTWAREASN A:216 , GLN A:217 , GLU A:218 , PHE A:229binding site for residue OSM A 728
24AE6SOFTWARESEP A:198 , LEU A:199 , ARG A:202 , LYS A:474binding site for residue GOL A 729
25AE7SOFTWAREASN A:95 , ILE A:315 , SCN A:708binding site for Mono-Saccharide NAG A 701 bound to ASN A 95
26AE8SOFTWAREASN A:205 , SER A:208 , ALA A:214 , VAL A:215 , GLN A:217 , HOH A:857 , HOH A:885binding site for Mono-Saccharide NAG A 702 bound to ASN A 205
27AE9SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , HOH A:824 , HOH A:945 , HOH A:1059binding site for Poly-Saccharide residues NAG A 703 through NAG A 704 bound to ASN A 241
28AF1SOFTWAREASN A:332 , HOH A:804 , HOH A:806binding site for Mono-Saccharide NAG A 705 bound to ASN A 332

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:167
2A:15 -A:28
3A:129 -A:139
4A:133 -A:157
5A:237 -A:248
6A:456 -A:513
7A:554 -A:579

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Cys A:6 -Gly A:7
2Pro A:9 -Val A:10
3Tyr A:172 -Gln A:173
4Lys A:233 -Pro A:234
5Tyr A:572 -Pro A:573

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GLS)

(-) 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:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhhh........eeeeeehhhhhhhhhhhhhhh...........hhhhhhhhhh........ee....hhhhhhhh.ee.....................ee.......hhhhhh.hhhhhhhhee......ee.....................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..............hhhhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gls A   1 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPsLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDSRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQKKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKMSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN 595
                                    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       480       490       500       510       520       530       540       550       560       570       580       590     
                                                                                                                                                                                                                               198-SEP
   Legend:   → Mismatch (orange background)
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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 5GLS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        PERL_BOVIN | P80025: 2gj1 2ips 2nqx 2pt3 2pum 2qpk 2qqt 2qrb 3bxi 3eri 3gc1 3gcj 3gck 3gcl 3i6n 3krq 3nyh 3ogw 3py4 3q9k 3ql6 3r4x 3r5o 3s4f 3tgy 3tuw 3uba 3v6q 4gm7 4gn6 4ksz 4njb 4nt3 4pnx 5b72 5gh0 5wv3

(-) Related Entries Specified in the PDB File

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