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(-) Description

Title :  CRYSTAL STRUCTURE OF LOV2-ZDK1 - THE COMPLEX OF OAT LOV2 AND THE AFFIBODY PROTEIN ZDARK1
 
Authors :  A. Winkler, H. Wang, E. Hartmann, K. Hahn, I. Schlichting
Date :  10 Sep 14  (Deposition) - 20 Jul 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Lov Domain, Photoreceptor, Affibody, Optogenetic Tool, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, M. Vilela, A. Winkler, M. Tarnawski, I. Schlichting, H. Yumerefendi, B. Kuhlman, R. Liu, G. Danuser, K. M. Hahn
Lovtrap: An Optogenetic System For Photoinduced Protein Dissociation.
Nat. Methods V. 13 755 2016
PubMed-ID: 27427858  |  Reference-DOI: 10.1038/NMETH.3926

(-) Compounds

Molecule 1 - NPH1-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 404-546
    Gene: NPH1-1
    Mutation: YES
    Organism Common: OAT
    Organism Scientific: AVENA SATIVA
    Organism Taxid: 4498
    Other Details: CYS450ALA MUTATION INTRODUCED TO RENDER THE PROTEIN LIGHT INACTIVE
 
Molecule 2 - Z-DARK, A SMALL PROTEIN BASED ON THE Z DOMAIN AFFIBODY
    Chains: B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: SELECTED FROM AN IN VITRO SELECTION FROM A PROTEIN DOMAIN LIBRARY USING MRNA DISPLAY BASED ON THE Z DOMAIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:416 , THR A:418 , ASN A:425 , ASN A:449 , ALA A:450 , ARG A:451 , LEU A:453 , GLN A:454 , VAL A:463 , ILE A:470 , LEU A:480 , ASN A:482 , ASN A:492 , PHE A:494 , LEU A:496 , PHE A:509 , ILE A:510 , GLY A:511 , GLN A:513 , HOH A:704 , HOH A:708 , LYS B:58binding site for residue FMN A 601
2AC2SOFTWAREASP A:501 , GLN A:502 , HOH A:732binding site for residue SO4 A 602
3AC3SOFTWAREARG A:410 , GLU A:412 , LYS A:413 , ARG A:448 , HOH A:715 , HOH A:717binding site for residue SO4 A 603
4AC4SOFTWAREGLU A:475 , ARG A:500 , HOH A:705binding site for residue SO4 A 604
5AC5SOFTWAREGLU A:475 , THR A:477 , HIS A:495 , ARG A:526 , LYS A:533 , HOH A:702 , HOH A:748binding site for residue SO4 A 605
6AC6SOFTWAREGLU A:443 , HOH A:715 , ASN B:23 , VAL B:24 , HOH B:201binding site for residue SO4 B 101
7AC7SOFTWAREGLN B:40 , ASN B:43 , LYS C:50binding site for residue SO4 B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EFW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EFW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EFW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EFW)

(-) 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:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5efw A 406 TTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKEL 546
                                   415       425       435       445       455       465       475       485       495       505       515       525       535       545 


Chain B from PDB  Type:PROTEIN  Length:55
                                                                                       
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 5efw B   4 KFNKEKTRAGAEIHSLPNLNVEQKFAFIVSLFDDPSQSANLLAEAKKLNDAQAPK  58
                                    13        23        33        43        53     


Chain C from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 5efw C  10 TRAGAEIHSLPNLNVEQKFAFIVSLFDDPSQSANLLAEAKKLNDAQAPK  58
                                    19        29        39        49
   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 5EFW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
        O49003_AVESA | O49003: 2v0u 2v0w 2v1a 2v1b 2wkp 2wkq 2wkr 4wf0 5hzh 5hzi 5hzj 5hzk

(-) Related Entries Specified in the PDB File

1lp1 2v0u