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(-) Description

Title :  TWO WAY MODE OF BINDING OF ANTITHYROID DRUG METHIMAZOLE TO MAMMALIAN HEME PEROXIDASES: STRUCTURE OF THE COMPLEX OF LACTOPEROXIDASE WITH METHIMAZOLE AT 1.97 ANGSTROM RESOLUTION
 
Authors :  R. P. Singh, A. Singh, H. Sirohi, A. K. Singh, P. Kaur, S. Sharma, T. P. Sin
Date :  17 Dec 15  (Deposition) - 13 Jan 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Singh, A. Singh, H. V. Sirohi, A. K. Singh, P. Kaur, S. Sharma, T. P. Singh
Dual Binding Mode Of Antithyroid Drug Methimazole To Mammalian Heme Peroxidases - Structural Determination Of Th Lactoperoxidase-Methimazole Complex At 1. 97 Angstrom Resolution.
Febs Open Bio V. 6 640 2016
PubMed-ID: 27398304  |  Reference-DOI: 10.1002/2211-5463.12051

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A, B
    Fragment: UNP RESIDUES 118-712
    Organism Common: GOAT
    Organism Scientific: CAPRA HIRCUS
    Organism Taxid: 9925

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 34)

Asymmetric Unit (6, 34)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MMZ4Ligand/Ion1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE
5NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NO39Ligand/IonNITRATE ION
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MMZ2Ligand/Ion1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NO35Ligand/IonNITRATE ION
Biological Unit 2 (5, 16)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MMZ2Ligand/Ion1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NO34Ligand/IonNITRATE ION

(-) Sites  (47, 47)

Asymmetric Unit (47, 47)
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 , GLN A:423 , ILE A:436 , ARG A:440 , MMZ A:601 , MMZ A:602 , HOH A:703 , HOH A:817binding site for residue HEM A 607
02AC2SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190binding site for residue CA A 608
03AC3SOFTWAREALA 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:802binding site for residue NO3 A 609
04AC4SOFTWAREASN A:241 , THR A:242 , THR A:243 , HOH A:858binding site for residue NO3 A 610
05AC5SOFTWARELEU A:92 , LYS A:402 , ASN A:403 , HOH A:779 , HOH A:820 , HOH A:979binding site for residue NO3 A 611
06AC6SOFTWAREILE A:306 , PHE A:309 , ARG A:310 , TRP A:529 , TRP A:530 , GLU A:531binding site for residue NO3 A 612
07AC7SOFTWAREASN A:408 , ASN A:410 , LYS A:411binding site for residue NO3 A 613
08AC8SOFTWAREGLU A:52 , PHE A:59 , GLY A:60 , TRP A:61 , THR A:62 , LYS A:65 , ARG A:71 , VAL A:72binding site for residue GOL A 614
09AC9SOFTWAREGLU A:52 , LYS A:65 , THR A:66 , HOH A:708binding site for residue GOL A 615
10AD1SOFTWAREALA A:56 , TRP A:61 , ASP A:137 , ARG A:162 , HOH A:755binding site for residue GOL A 616
11AD2SOFTWAREGLU A:116 , GLU A:118 , PRO A:159 , PHE A:160 , PHE A:161 , GLN A:423 , HIS A:426 , PHE A:431 , ILE A:436binding site for residue GOL A 617
12AD3SOFTWAREMET 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 , LEU B:433 , ILE B:436 , ARG B:440 , MMZ B:601 , MMZ B:613 , HOH B:726 , HOH B:735binding site for residue HEM B 607
13AD4SOFTWAREASP B:110 , THR B:184 , PHE B:186 , ASP B:188 , SER B:190binding site for residue CA B 608
14AD5SOFTWAREALA 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:706binding site for residue NO3 B 609
15AD6SOFTWAREARG B:76 , PRO B:149 , LYS B:150 , ASN B:419 , HOH B:788 , HOH B:864binding site for residue NO3 B 610
16AD7SOFTWAREASP B:311 , HIS B:565 , ALA B:566 , PHE B:567 , HOH B:867binding site for residue NO3 B 611
17AD8SOFTWARELEU B:92 , LYS B:402 , ASN B:403 , HOH B:709 , HOH B:785binding site for residue NO3 B 612
18AD9SOFTWAREALA B:56 , VAL B:57 , TRP B:61 , ASP B:137 , ARG B:162 , HOH B:897binding site for residue GOL B 614
19AE1SOFTWAREGLU B:52 , PHE B:59 , GLY B:60 , TRP B:61 , THR B:62 , LYS B:65 , THR B:66 , ARG B:71 , VAL B:72binding site for residue GOL B 615
20AE2SOFTWAREGLU B:52 , PHE B:59 , LYS B:65 , THR B:66binding site for residue GOL B 616
21AE3SOFTWAREASN B:532 , PRO B:533 , GLY B:534 , HOH B:718 , HOH B:873binding site for residue GOL B 617
22AE4SOFTWAREASN A:95 , HOH A:707binding site for Mono-Saccharide NAG A 604 bound to ASN A 95
23AE5SOFTWAREASN A:205 , SER A:208 , LEU A:210 , ALA A:214 , VAL A:215 , GLN A:217 , HOH A:706 , HOH A:732 , HOH A:735 , HOH A:801 , HOH A:991binding site for Mono-Saccharide NAG A 606 bound to ASN A 205
24AE6SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , HOH A:714 , HOH A:758binding site for Mono-Saccharide NAG A 603 bound to ASN A 241
25AE7SOFTWAREASN A:332 , SER A:334 , HOH A:880binding site for Mono-Saccharide NAG A 605 bound to ASN A 332
26AE8SOFTWAREASN B:95 , HOH B:702binding site for Mono-Saccharide NAG B 602 bound to ASN B 95
27AE9SOFTWAREASN B:205 , SER B:208 , LEU B:210 , ALA B:214 , VAL B:215 , GLN B:217 , TRP B:220 , HOH B:756 , HOH B:896binding site for Poly-Saccharide residues NAG B 605 through NAG B 606 bound to ASN B 205
28AF1SOFTWAREASN B:241 , ALA B:244 , TRP B:384 , HOH B:710 , HOH B:947binding site for Mono-Saccharide NAG B 603 bound to ASN B 241
29AF2SOFTWAREASN B:332 , SER B:334 , HOH B:795binding site for Mono-Saccharide NAG B 604 bound to ASN B 332
30AF3SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
31AF4SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
32AF5SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
33AF6SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
34AF7SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
35AF8SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
36AF9SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
37AG1SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
38AG2SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
39AG3SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:607 , HOH A:701 , HOH A:1084binding site for residues MMZ A 601 and MMZ A 602
40AG4SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
41AG5SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
42AG6SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
43AG7SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
44AG8SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
45AG9SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
46AH1SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613
47AH2SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , GLU B:258 , HEM B:607 , HOH B:701 , HOH B:1033 , HOH B:1042binding site for residues MMZ B 601 and MMZ B 613

(-) SS Bonds  (14, 14)

Asymmetric 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 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 5FF1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FF1)

(-) Exons   (0, 0)

(no "Exon" information available for 5FF1)

(-) 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: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......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ff1 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.hhhhhhhhh..............................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhh..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
                 5ff1 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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  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 5FF1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FF1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FF1)

(-) Gene Ontology  (9, 9)

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        A3F9D6_CAPHI | A3F9D6: 2e9e 2efb 2eha 2ojv 2r5l 3n8f 3nak 3niu 3qf1 3r55 3rke 3sxv 4ig5 4ljj 4msf 4n7a 4oek 4qjq 4qyq 5hpw

(-) Related Entries Specified in the PDB File

4qjq