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(-) Description

Title :  CRYSTAL STRUCTURE OF BUFFALO LACTOPEROXIDASE WITH RHODANIDE AT 2.09 ANGSTROM RESOLUTION
 
Authors :  A. Gupta, T. K. Tyagi, P. Kaur, S. Sharma, T. P. Singh
Date :  11 Feb 15  (Deposition) - 25 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Lactoperoxidase, Oxidoreductase, Substrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gupta, T. K. Tyagi, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of Buffalo Lactoperoxidase With Rhodanide At 2. 09 Angstrom Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Organism Scientific: BUBALUS BUBALIS
    Organism Taxid: 89462

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 27)

Asymmetric/Biological Unit (9, 27)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IOD6Ligand/IonIODIDE ION
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NO34Ligand/IonNITRATE ION
8SCN4Ligand/IonTHIOCYANATE ION
9SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190binding site for residue CA A 611
02AC2SOFTWAREPHE A:229binding site for residue IOD A 612
03AC3SOFTWAREPRO A:236 , PRO A:424binding site for residue IOD A 613
04AC4SOFTWAREARG A:397 , LYS A:561binding site for residue IOD A 614
05AC5SOFTWARETRP A:46 , VAL A:342binding site for residue IOD A 615
06AC6SOFTWARELYS A:462 , THR A:463binding site for residue IOD A 616
07AC7SOFTWARETYR A:85 , LEU A:86 , ASP A:87 , LYS A:411 , HOH A:840binding site for residue NO3 A 617
08AC8SOFTWAREARG A:31 , TYR A:331 , ARG A:527 , HOH A:715binding site for residue NO3 A 618
09AC9SOFTWAREGLU A:77 , ASN A:80 , PRO A:145binding site for residue NO3 A 619
10AD1SOFTWAREHIS A:377 , HIS A:429 , HOH A:731binding site for residue NO3 A 620
11AD2SOFTWAREMET 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 , LEU A:417 , GLN A:423 , LEU A:433 , ILE A:436 , ARG A:440 , SCN A:624 , HOH A:760 , HOH A:869binding site for residue HEM A 621
12AD3SOFTWARESER A:359 , LEU A:361 , PRO A:367 , LYS A:402binding site for residue SCN A 622
13AD4SOFTWAREPRO A:149 , ASN A:419binding site for residue SCN A 623
14AD5SOFTWAREARG A:255 , HEM A:621 , HOH A:868 , HOH A:869binding site for residue SCN A 624
15AD6SOFTWARESEP A:198 , ARG A:202binding site for residue SCN A 625
16AD7SOFTWARETRP A:530binding site for residue IOD A 626
17AD8SOFTWAREASN A:95 , ARG A:96 , ARG A:504 , HIS A:565 , GLN A:568 , HOH A:810 , HOH A:820 , HOH A:831binding site for Poly-Saccharide residues NAG A 601 through BMA A 603 bound to ASN A 95
18AD9SOFTWAREASN A:205 , SER A:208 , VAL A:215 , GLN A:217 , TRP A:220 , HOH A:833binding site for Poly-Saccharide residues NAG A 604 through NAG A 605 bound to ASN A 205
19AE1SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , HOH A:706 , HOH A:759binding site for Poly-Saccharide residues NAG A 606 through MAN A 608 bound to ASN A 241
20AE2SOFTWAREASN A:332binding site for Poly-Saccharide residues NAG A 609 through NAG A 610 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  (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 4Y55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y55)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y55)

(-) 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.............hhhhhhhhhhhhhhhh.............hhhhhhhh........ee....hhhhhhhh.ee.....................ee.......hhhhhh.hhhhhhhh...............................hhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhh...........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y55 A   1 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEDGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPsLASRLQNLSSPLGLMAVNQEAWDHGLAYLPFNNRKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPQWDGEKLYQEARKILGAFVQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKMSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAVDKLDLSPWASREN 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
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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 4Y55)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y55)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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        PERL_BUBBU | A5JUY8: 2gjm 2o86 2z5z 3erh 3faq 3fnl

(-) Related Entries Specified in the PDB File

2o86 CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF BUFFALO LACTOPEROXIDASE WITH NITRATE AND IODIDE AT 2.8 A RESOLUTION