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(-) Description

Title :  PREDICTING PROTEIN CONFORMATIONAL RESPONSE IN PROSPECTIVE LIGAND DISCOVERY
 
Authors :  M. Fischer, J. S. Fraser
Date :  05 Dec 13  (Deposition) - 18 Dec 13  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Model System, Flexibility, Dynamic, Loop, Side-Chains, Energy Penalty, Occupancy, Boltzmann Weights, Flexible Docking, Ligand Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fischer, R. G. Coleman, J. S. Fraser, B. K. Shoichet
Incorporation Of Protein Flexibility And Conformational Energy Penalties In Docking Screens To Improve Ligand Discovery.
Nat Chem V. 6 575 2014
PubMed-ID: 24950326  |  Reference-DOI: 10.1038/NCHEM.1954

(-) Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 72-362
    Gene: CCP1 CCP CPO YKR066C, SCRG_04081
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 285006
    Strain: RM11-1A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:44 , ARG A:48 , TRP A:51 , PRO A:145 , ASP A:146 , ALA A:147 , LEU A:171 , ALA A:174 , HIS A:175 , GLY A:178 , LYS A:179 , THR A:180 , HIS A:181 , ASN A:184 , SER A:185 , LEU A:230 , THR A:232 , HOH A:427 , HOH A:433 , HOH A:438 , HOH A:444BINDING SITE FOR RESIDUE HEM A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NVA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NVA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NVA)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4nvaa_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhheeehhhhhh..eeeee....hhhhhhhhhh..eeee.....eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nva A   4 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGGGANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 292
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        B3LRE1_YEAS1 | B3LRE1: 4jm5 4jm6 4jm8 4jm9 4jma 4jmb 4jms 4jmt 4jmv 4jmw 4jmz 4jn0 4jpl 4jpt 4jpu 4jqj 4jqk 4jqm 4jqn 4nvb 4nvc 4nvd 4nve 4nvf 4nvg 4nvh 4nvi 4nvj 4nvk 4nvl 4nvm 4nvn 4nvo 4oq7 5u5u 5u5v 5u5w 5u5x 5u5y 5u5z 5u60 5u61 5ug2

(-) Related Entries Specified in the PDB File

4nvb 4nvc 4nvd 4nve 4nvf 4nvg 4nvh 4nvi 4nvj 4nvk 4nvl 4nvm 4nvn 4nvo