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 AN ENGINEERED METAL-FREE RIDC1 VARIANT CONTAINING FIVE DISULFIDE BONDS.
 
Authors :  F. A. Tezcan, L. A. Churchfield
Date :  02 Aug 16  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Engineered Protein, Cytochrome, Complex, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Churchfield, A. Medina-Morales, J. D. Brodin, A. Perez, F. A. Tezcan
De Novo Design Of An Allosteric Metalloprotein Assembly Wit Strained Disulfide Bonds.
J. Am. Chem. Soc. V. 138 13163 2016
PubMed-ID: 27649076  |  Reference-DOI: 10.1021/JACS.6B08458

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562
    Chains: A, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 23-128
    Gene: CYBC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562
 
Molecule 2 - SOLUBLE CYTOCHROME B562
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 23-128
    Gene: CYBC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:4 , MET A:7 , ASN A:11 , LEU A:14 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , ARG A:106binding site for residue HEM A 201
2AC2SOFTWAREMET B:7 , GLU B:8 , ASN B:11 , PRO B:45 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106binding site for residue HEM B 201
3AC3SOFTWAREASN A:99 , GLU B:49 , ASP B:50 , HOH B:319binding site for residue NA B 202
4AC4SOFTWAREGLU C:4binding site for residue NA C 202
5AC5SOFTWAREGLU C:4 , MET C:7 , ASN C:11 , PHE C:61 , PHE C:65 , THR C:97 , CYS C:98 , ASN C:99 , ALA C:100 , HIS C:102 , GLN C:103 , LYS C:104 , TYR C:105 , ARG C:106binding site for Di-peptide HEM C 201 and CYS C 101
6AC6SOFTWAREGLU C:4 , MET C:7 , ASN C:11 , PHE C:61 , PHE C:65 , LEU C:94 , LYS C:95 , CYS C:96 , THR C:97 , ASN C:99 , ALA C:100 , CYS C:101 , HIS C:102 , TYR C:105 , ARG C:106binding site for Di-peptide HEM C 201 and CYS C 98
7AC7SOFTWAREGLU D:4 , MET D:7 , LEU D:10 , ASN D:11 , PHE D:61 , PHE D:65 , THR D:97 , CYS D:98 , ASN D:99 , ALA D:100 , HIS D:102 , GLN D:103 , LYS D:104 , TYR D:105 , ARG D:106 , HOH D:302binding site for Di-peptide HEM D 201 and CYS D 101
8AC8SOFTWAREGLU D:4 , MET D:7 , LEU D:10 , ASN D:11 , PHE D:61 , PHE D:65 , LEU D:94 , LYS D:95 , CYS D:96 , THR D:97 , ASN D:99 , ALA D:100 , CYS D:101 , HIS D:102 , ARG D:106 , HOH D:302binding site for Di-peptide HEM D 201 and CYS D 98

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:38 -C:38
2A:81 -D:81
3A:96 -B:96
4B:81 -C:81
5C:96 -D:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L31)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L31)

(-) Exons   (0, 0)

(no "Exon" information available for 5L31)

(-) 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:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5l31 A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAACDAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5l31 B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAcDAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30       |40        50        60        70        80        90       100      
                                                                38-CSO                                                                


Chain C from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5l31 C   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAACDAWSATPPSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40     || 55        65        75        85        95       105 
                                                                        46|                                                      
                                                                         52                                                      


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5l31 D   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAACDAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100
   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 5L31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L31)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L31)

(-) Gene Ontology  (7, 7)

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
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l31)
 

(-) 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
  5l31
    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
  C562_ECOLX | P0ABE7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  C562_ECOLX | P0ABE7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L31)