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(-) Description

Title :  CRYSTAL STRUCTURE OF METHIMAZOLE INHIBITED DIMERIC GOAT LACTOPEROXIDASE AT 1.97A RESOLUTION
 
Authors :  R. P. Singh, N. Singh, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Sing
Date :  16 Dec 12  (Deposition) - 05 Jun 13  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lactoperoxidase, Heme, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Singh, A. Singh, G. S. Kushwaha, A. K. Singh, P. Kaur, S. Sharma, T. P. Singh
Mode Of Binding Of The Antithyroid Drug Propylthiouracil To Mammalian Haem Peroxidases
Acta Crystallogr. , Sect. F V. 71 304 2015
PubMed-ID: 25760705  |  Reference-DOI: 10.1107/S2053230X15001806

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 33)

Asymmetric/Biological Unit (6, 33)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MMZ2Ligand/Ion1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE
5NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NO39Ligand/IonNITRATE ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET 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 , VAL A:354 , PHE A:380 , GLN A:423 , ILE A:436 , ARG A:440 , MMZ A:616 , HOH A:869 , HOH A:937BINDING SITE FOR RESIDUE HEM A 601
02AC2SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , HOH A:934 , HOH A:1070 , HOH A:1086BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWAREASN A:95 , ARG A:96 , GLN A:568BINDING SITE FOR RESIDUE NAG A 603
04AC4SOFTWAREASN A:332 , HOH A:1121 , HOH A:1128BINDING SITE FOR RESIDUE NAG A 604
05AC5SOFTWAREASN A:205 , SER A:208 , LEU A:210 , ALA A:214 , VAL A:215 , GLN A:217 , HOH A:791 , HOH A:826 , HOH A:847 , HOH A:849 , HOH A:910BINDING SITE FOR RESIDUE NAG A 605
06AC6SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 606
07AC7SOFTWAREALA A:44 , ARG A:45 , TRP A:46 , LEU A:47 , SER A:340 , ASN A:341 , VAL A:342 , MET A:446 , TRP A:452 , HOH A:714BINDING SITE FOR RESIDUE NO3 A 607
08AC8SOFTWAREILE A:240 , ASN A:241 , THR A:242 , THR A:243 , HOH A:1077BINDING SITE FOR RESIDUE NO3 A 608
09AC9SOFTWARELEU A:92 , LYS A:402 , ASN A:403 , HOH A:922 , HOH A:961 , HOH A:989 , HOH A:1011BINDING SITE FOR RESIDUE NO3 A 609
10BC1SOFTWAREILE A:306 , PHE A:309 , TRP A:529 , TRP A:530 , GLU A:531BINDING SITE FOR RESIDUE NO3 A 610
11BC2SOFTWAREASN A:408 , ASN A:410 , LYS A:411 , HOH A:1002BINDING SITE FOR RESIDUE NO3 A 611
12BC3SOFTWAREGLU A:52 , PHE A:59 , GLY A:60 , TRP A:61 , THR A:62 , LYS A:65 , THR A:66 , ARG A:71 , VAL A:72BINDING SITE FOR RESIDUE GOL A 612
13BC4SOFTWAREGLU A:52 , LYS A:65 , THR A:66BINDING SITE FOR RESIDUE GOL A 613
14BC5SOFTWAREALA A:56 , VAL A:57 , TRP A:61 , ASP A:137 , ARG A:162 , HOH A:793BINDING SITE FOR RESIDUE GOL A 614
15BC6SOFTWAREGLU A:116 , GLU A:118 , PRO A:159 , PHE A:161 , GLN A:423 , HIS A:426 , ILE A:436BINDING SITE FOR RESIDUE GOL A 615
16BC7SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:601 , HOH A:728BINDING SITE FOR RESIDUE MMZ A 616
17BC8SOFTWAREASP B:110 , THR B:184 , PHE B:186 , ASP B:188 , SER B:190BINDING SITE FOR RESIDUE CA B 601
18BC9SOFTWAREMET B:101 , GLY B:104 , GLN B:105 , ASP B:108 , ASP B:112 , PHE B:113 , ALA B:114 , ARG B:255 , GLU B:258 , GLN B:259 , THR B:344 , PHE B:347 , ARG B:348 , GLY B:350 , HIS B:351 , VAL B:354 , PHE B:380 , GLN B:423 , LEU B:433 , ILE B:436 , ARG B:440 , MMZ B:617 , HOH B:793 , HOH B:887BINDING SITE FOR RESIDUE HEM B 602
19CC1SOFTWAREASN B:95 , ARG B:96 , ILE B:315 , HOH B:830 , HOH B:936 , HOH B:1030BINDING SITE FOR RESIDUE NAG B 603
20CC2SOFTWAREASN B:332 , SER B:334 , HOH B:922BINDING SITE FOR RESIDUE NAG B 606
21CC3SOFTWAREALA B:44 , ARG B:45 , TRP B:46 , LEU B:47 , SER B:340 , ASN B:341 , VAL B:342 , MET B:446 , TRP B:452 , HOH B:716BINDING SITE FOR RESIDUE NO3 B 609
22CC4SOFTWAREARG B:76 , PRO B:149 , LYS B:150 , ASN B:419 , HOH B:806 , HOH B:988BINDING SITE FOR RESIDUE NO3 B 610
23CC5SOFTWAREHIS B:565 , ALA B:566 , PHE B:567 , GLN B:568BINDING SITE FOR RESIDUE NO3 B 611
24CC6SOFTWARELEU B:92 , LYS B:402 , ASN B:403 , HOH B:895 , HOH B:912BINDING SITE FOR RESIDUE NO3 B 612
25CC7SOFTWAREALA B:56 , VAL B:57 , TRP B:61 , ASP B:137 , ARG B:162 , HOH B:929BINDING SITE FOR RESIDUE GOL B 613
26CC8SOFTWAREGLU B:52 , PHE B:59 , GLY B:60 , TRP B:61 , THR B:62 , LYS B:65 , ARG B:71 , VAL B:72BINDING SITE FOR RESIDUE GOL B 614
27CC9SOFTWAREGLU B:52 , PHE B:59 , LYS B:65 , THR B:66BINDING SITE FOR RESIDUE GOL B 615
28DC1SOFTWAREARG B:527 , ASN B:532 , PRO B:533 , HOH B:976BINDING SITE FOR RESIDUE GOL B 616
29DC2SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:602 , HOH B:984BINDING SITE FOR RESIDUE MMZ B 617
30DC3SOFTWAREASN B:241 , ALA B:244 , TRP B:384 , HOH B:800BINDING SITE FOR LINKED RESIDUES B 604 to 605
31DC4SOFTWAREASN B:205 , SER B:208 , LEU B:210 , ALA B:214 , VAL B:215 , GLN B:217 , HOH B:781 , HOH B:839BINDING SITE FOR LINKED RESIDUES B 607 to 608

(-) SS Bonds  (14, 14)

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
8B:6 -B:167
9B:15 -B:28
10B:129 -B:139
11B:133 -B:157
12B:237 -B:248
13B:456 -B:513
14B:554 -B:579

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:170 -Pro A:171
2Lys A:233 -Pro A:234
3Tyr A:572 -Pro A:573
4Trp B:2 -Glu B:3
5Lys B:233 -Pro B:234
6Tyr B:572 -Pro B:573

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IG5)

(-) Exons   (0, 0)

(no "Exon" information available for 4IG5)

(-) 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....hhhhhh...ee.....................ee.......hhhhhh.hhhhhhhhh..............................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..............hhhhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee............eee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ig5 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     


Chain B 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.....hhhhhh..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
                 4ig5 B   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
   Legend:   → Mismatch (orange background)
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    → 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 4IG5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IG5)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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        A3F9D6_CAPHI | A3F9D6: 2e9e 2efb 2eha 2ojv 2r5l 3n8f 3nak 3niu 3qf1 3r55 3rke 3sxv 4ljj 4msf 4n7a 4oek 4qjq 4qyq 5ff1 5hpw

(-) Related Entries Specified in the PDB File

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3sxv CRYSTAL STRUCTURE OF THE COMPLEX OF GOAT LACTOPEROXIDASE WITH AMITROLE AT 2.1 A RESOLUTION