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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF GOAT LACTOPEROXIDASE WITH PYRAZINAMIDE AT 2.1 A RESOLUTION
 
Authors :  R. P. Singh, N. Pandey, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Sin
Date :  18 Mar 11  (Deposition) - 03 Aug 11  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Goat Lactoperoxidase, Oxidoreductase, Piperazine, Iodide, Edo, Pyrazinamide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Singh, N. Pandey, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Goat Lactoperoxidase With Pyrazinamide At 2. 1 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Fragment: UNP RESIDUES 118-712
    Organism Common: DOMESTIC GOAT,GOATS
    Organism Scientific: CAPRA HIRCUS
    Organism Taxid: 9925

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 34)

Asymmetric/Biological Unit (12, 34)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IOD12Ligand/IonIODIDE ION
6MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9PZA2Ligand/IonPYRAZINE-2-CARBOXAMIDE
10SCN1Ligand/IonTHIOCYANATE ION
11SEP1Mod. Amino AcidPHOSPHOSERINE
12ZN1Ligand/IonZINC ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:95 , PRO A:209 , ILE A:315 , HOH A:767BINDING SITE FOR RESIDUE NAG A 596
02AC2SOFTWAREASN A:205 , SER A:208 , LEU A:210 , ALA A:214 , VAL A:215 , GLN A:217 , NAG A:600 , HOH A:712BINDING SITE FOR RESIDUE NAG A 599
03AC3SOFTWARENAG A:599 , HOH A:910BINDING SITE FOR RESIDUE NAG A 600
04AC4SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , LYS A:388 , NAG A:602 , HOH A:679 , HOH A:932 , HOH A:933BINDING SITE FOR RESIDUE NAG A 601
05AC5SOFTWARENAG A:601BINDING SITE FOR RESIDUE NAG A 602
06AC6SOFTWAREASN A:332 , SER A:334 , VAL A:335 , HOH A:818BINDING SITE FOR RESIDUE NAG A 604
07AC7SOFTWAREMET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , GLU A:258 , GLN A:259 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , VAL A:354 , PHE A:380 , LEU A:417 , GLN A:423 , LEU A:433 , ILE A:436 , ARG A:440 , PZA A:597 , PZA A:598 , HOH A:836BINDING SITE FOR RESIDUE HEM A 618
08AC8SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 607
09AC9SOFTWAREHIS A:222 , HIS A:558BINDING SITE FOR RESIDUE ZN A 608
10BC1SOFTWARETRP A:46 , VAL A:342 , TRP A:452BINDING SITE FOR RESIDUE IOD A 609
11BC2SOFTWAREPHE A:229BINDING SITE FOR RESIDUE IOD A 610
12BC3SOFTWAREARG A:397BINDING SITE FOR RESIDUE IOD A 611
13BC4SOFTWAREASN A:80BINDING SITE FOR RESIDUE IOD A 612
14BC5SOFTWAREARG A:96BINDING SITE FOR RESIDUE IOD A 613
15BC6SOFTWARELYS A:462BINDING SITE FOR RESIDUE IOD A 616
16BC7SOFTWAREALA A:566 , PHE A:567BINDING SITE FOR RESIDUE IOD A 617
17BC8SOFTWAREALA A:225BINDING SITE FOR RESIDUE IOD A 620
18BC9SOFTWAREGLU A:373BINDING SITE FOR RESIDUE IOD A 624
19CC1SOFTWAREPRO A:236 , THR A:425BINDING SITE FOR RESIDUE IOD A 626
20CC2SOFTWAREASN A:230BINDING SITE FOR RESIDUE SCN A 700
21CC3SOFTWAREGLN A:105 , ASP A:108 , HIS A:109 , ARG A:255 , GLU A:258 , PZA A:598 , HEM A:618 , HOH A:836BINDING SITE FOR RESIDUE PZA A 597
22CC4SOFTWARESER A:254 , GLU A:258 , PHE A:381 , PZA A:597 , HEM A:618BINDING SITE FOR RESIDUE PZA A 598
23CC5SOFTWAREHIS A:377 , HIS A:429 , HOH A:935BINDING SITE FOR RESIDUE EDO A 603
24CC6SOFTWARESER A:33 , ALA A:35 , LEU A:36 , ARG A:41 , HOH A:677 , HOH A:809BINDING SITE FOR RESIDUE EDO A 605
25CC7SOFTWAREPRO A:197 , LYS A:472BINDING SITE FOR RESIDUE EDO A 606
26CC8SOFTWAREALA A:219 , PHE A:229 , VAL A:246BINDING SITE FOR RESIDUE EDO A 614
27CC9SOFTWARESER A:359 , LEU A:361 , PRO A:367 , GLU A:373 , LYS A:402 , HOH A:911BINDING SITE FOR RESIDUE EDO A 619
28DC1SOFTWAREARG A:76 , ASN A:80 , PRO A:149 , ARG A:418 , ASN A:419BINDING SITE FOR RESIDUE GOL A 621
29DC2SOFTWAREGLU A:123 , SER A:125 , CYS A:129 , ASP A:137 , GLU A:138 , CYS A:139 , PHE A:161BINDING SITE FOR RESIDUE GOL A 622
30DC3SOFTWARESEP A:198 , LEU A:199 , ARG A:202 , ASN A:473 , LYS A:474 , VAL A:475BINDING SITE FOR RESIDUE MRD A 623
31DC4SOFTWARELYS A:81 , LYS A:479 , ASP A:482 , LEU A:483 , HOH A:658BINDING SITE FOR RESIDUE PEG A 625

(-) 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  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:233 -Pro A:234
2Tyr A:572 -Pro A:573

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R55)

(-) Exons   (0, 0)

(no "Exon" information available for 3R55)

(-) 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
 aligned with A3F9D6_CAPHI | A3F9D6 from UniProtKB/TrEMBL  Length:712

    Alignment length:595
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707     
         A3F9D6_CAPHI   118 SWEVGCGAPVPLVTCDEQSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLAVPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSSEHSKVQCEEYCVQGDECFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLARDQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYPPFNNVKPSPCEFINTTAHVPCFQAGDSRASEQILLATVHTLLLREHNRLARELKRLNPHWDGEMLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKNSKLMNQNKMVTSELRNKLFQPTHKVHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQAVLKNKVLAKKLLDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAVDKLDLSPWASREN 712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhhh........eeeeeehhhhhhhhhhhhhhh...........hhhhhhhhhh........ee....hhhhhhh..ee.....................ee.......hhhhhh.hhhhhhhhh..............................hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee............eee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r55 A   1 SWEVGCGAPVPLVTCDEQSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLAVPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSSEHSKVQCEEYCVQGDECFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLARDQINAVTSFLDASLVYGSEPsLASRLRNLSSPLGLMAVNQEAWDHGLAYPPFNNVKPSPCEFINTTAHVPCFQAGDSRASEQILLATVHTLLLREHNRLARELKRLNPHWDGEMLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKNSKLMNQNKMVTSELRNKLFQPTHKVHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQAVLKNKVLAKKLLDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAVDKLDLSPWASREN 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)
  - → 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 3R55)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R55)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A3F9D6_CAPHI | A3F9D6)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0036393    thiocyanate peroxidase activity    Catalysis of the reaction: thiocyanate (SCN-) + hydrogen peroxide (H2O2) = hypothiocyanite (OSCN-) + 2 H2O. Catalyzes the hydrogen peroxide oxidation of thiocyanate.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0018969    thiocyanate metabolic process    The chemical reactions and pathways involving thiocyanate, the anion of thiocyanic acid, a toxic cyanide derivative commonly formed as a by-product in the production of gas for fuel, coke, and substances for chemical industries.

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  3r55
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  1.11.1.7
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 Related Entries

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

UniProtKB/TrEMBL
        A3F9D6_CAPHI | A3F9D6: 2e9e 2efb 2eha 2ojv 2r5l 3n8f 3nak 3niu 3qf1 3rke 3sxv 4ig5 4ljj 4msf 4n7a 4oek 4qjq 4qyq 5ff1 5hpw

(-) Related Entries Specified in the PDB File

2r5l CRYSTAL STRUCTURES OF GOAT LACTOPEROXIDASE
3r4x
3r5o
3r5q