Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF GOAT LACTOPEROXIDASE WITH ACRYLONITRILE AT 1.98 A RESOLUTION
 
Authors :  M. Kumar, R. P. Singh, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Sing
Date :  05 Jul 13  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kumar, R. P. Singh, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Goat Lactoperoxidase With Acrylonitrile At 1. 98 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: GOAT
    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  (11, 31)

Asymmetric/Biological Unit (11, 31)
No.NameCountTypeFull Name
16AC1Ligand/IonPROP-2-ENENITRILE
2CA1Ligand/IonCALCIUM ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6IOD13Ligand/IonIODIDE ION
7MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
8NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
9PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
10SCN1Ligand/IonTHIOCYANATE ION
11SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:95 , PRO A:209 , ILE A:315BINDING SITE FOR RESIDUE NAG A 601
02AC2SOFTWAREASN A:205 , SER A:208 , LEU A:210 , LEU A:212 , ALA A:214 , VAL A:215 , GLN A:217 , HOH A:781 , HOH A:950 , HOH A:958 , HOH A:1004BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , NAG A:604 , HOH A:750BINDING SITE FOR RESIDUE NAG A 603
04AC4SOFTWARENAG A:603 , HOH A:967BINDING SITE FOR RESIDUE NAG A 604
05AC5SOFTWAREASN A:332 , VAL A:335BINDING SITE FOR RESIDUE NAG A 605
06AC6SOFTWAREMET 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 , 6AC A:629 , HOH A:995 , HOH A:1011BINDING SITE FOR RESIDUE HEM A 606
07AC7SOFTWAREARG A:397 , THR A:560BINDING SITE FOR RESIDUE IOD A 608
08AC8SOFTWAREASN A:80BINDING SITE FOR RESIDUE IOD A 609
09AC9SOFTWAREARG A:96BINDING SITE FOR RESIDUE IOD A 610
10BC1SOFTWARELEU A:12 , LYS A:462BINDING SITE FOR RESIDUE IOD A 612
11BC2SOFTWAREHIS A:565 , ALA A:566 , PHE A:567 , HOH A:981BINDING SITE FOR RESIDUE IOD A 613
12BC3SOFTWAREALA A:225 , HOH A:718BINDING SITE FOR RESIDUE IOD A 614
13BC4SOFTWAREGLU A:373BINDING SITE FOR RESIDUE IOD A 615
14BC5SOFTWAREPRO A:236 , THR A:425BINDING SITE FOR RESIDUE IOD A 616
15BC6SOFTWAREHOH A:788BINDING SITE FOR RESIDUE IOD A 617
16BC7SOFTWAREHIS A:377 , THR A:378 , HIS A:429BINDING SITE FOR RESIDUE EDO A 618
17BC8SOFTWARESER A:33 , ALA A:35 , ARG A:41 , ARG A:338 , HOH A:867BINDING SITE FOR RESIDUE EDO A 619
18BC9SOFTWAREPRO A:197 , LYS A:472BINDING SITE FOR RESIDUE EDO A 620
19CC1SOFTWAREGLU A:218 , PHE A:229 , VAL A:246BINDING SITE FOR RESIDUE EDO A 621
20CC2SOFTWARESER A:359 , LEU A:361 , LYS A:402BINDING SITE FOR RESIDUE EDO A 622
21CC3SOFTWAREARG A:76 , ASN A:80 , PRO A:149 , LYS A:150 , ARG A:418 , ASN A:419BINDING SITE FOR RESIDUE GOL A 623
22CC4SOFTWARESEP A:198 , LEU A:199 , ARG A:202 , ASN A:473 , LYS A:474BINDING SITE FOR RESIDUE MPD A 624
23CC5SOFTWARELYS A:81 , LYS A:479 , LEU A:483 , HOH A:729BINDING SITE FOR RESIDUE PEG A 625
24CC6SOFTWAREASN A:230 , CYS A:248 , HOH A:794BINDING SITE FOR RESIDUE SCN A 626
25CC7SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 627
26CC9SOFTWAREHIS A:109 , ARG A:255 , HEM A:606 , HOH A:1011 , HOH A:1013BINDING SITE FOR RESIDUE 6AC A 629
27DC1SOFTWARETRP A:46 , VAL A:342BINDING SITE FOR RESIDUE IOD A 630

(-) 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 4LJJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LJJ)

(-) 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...........hhhhhhhh..........ee....hhhhhhhh.ee.....................ee.......hhhhhh.hhhhhhhhee......ee.....................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee............eee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljj 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 4LJJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    6AC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:233 - Pro A:234   [ RasMol ]  
    Tyr A:572 - Pro A:573   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ljj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A3F9D6_CAPHI | A3F9D6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A3F9D6_CAPHI | A3F9D6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 3r55 3rke 3sxv 4ig5 4msf 4n7a 4oek 4qjq 4qyq 5ff1 5hpw

(-) Related Entries Specified in the PDB File

3sxv MODEL PDB