Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  GEPHE IN COMPLEX WITH MG(2+) - AMP
 
Authors :  V. B. Kasaragod, H. Schindelin
Date :  15 Nov 15  (Deposition) - 04 May 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Moco And Wco Biosynthesis, Moco, Amp With Mg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. B. Kasaragod, H. Schindelin
Structural Framework For Metal Incorporation During Molybdenum Cofactor Biosynthesis.
Structure V. 24 782 2016
PubMed-ID: 27112598  |  Reference-DOI: 10.1016/J.STR.2016.02.023

(-) Compounds

Molecule 1 - GEPHYRIN
    Chains: A
    EC Number: 2.7.7.75, 2.10.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 318-736
    Gene: GPHN, GPH
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PUTATIVE GLYCINE RECEPTOR-TUBULIN LINKER PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO42Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:505 , GLU A:509 , LEU A:510 , ILE A:522 , ASP A:524 , SER A:525 , ASN A:526 , GLY A:572 , GLY A:573 , ASP A:580 , GLY A:626 , ASN A:627 , PRO A:628 , MG A:802 , HOH A:902 , HOH A:929 , HOH A:938 , HOH A:1016 , HOH A:1044 , HOH A:1065 , HOH A:1118 , HOH A:1152 , HOH A:1157 , HOH A:1170binding site for residue AMP A 801
2AC2SOFTWAREAMP A:801 , HOH A:929 , HOH A:1028 , HOH A:1044 , HOH A:1157 , HOH A:1170binding site for residue MG A 802
3AC3SOFTWAREALA A:356 , HOH A:1153 , HOH A:1177binding site for residue ACT A 803
4AC4SOFTWARELEU A:323binding site for residue ACT A 804
5AC5SOFTWARECYS A:469 , ALA A:472binding site for residue ACT A 805
6AC6SOFTWAREARG A:564 , LYS A:619binding site for residue PO4 A 806
7AC7SOFTWARESER A:480 , HOH A:1007 , HOH A:1035 , HOH A:1377binding site for residue MPD A 807
8AC8SOFTWAREGLU A:514 , HOH A:901 , HOH A:1017 , HOH A:1226binding site for residue MPD A 808
9AC9SOFTWAREILE A:656 , MET A:711 , HOH A:944binding site for residue MPD A 809

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:365 -Pro A:366
2Lys A:602 -Pro A:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERS)

(-) Sequences/Alignments

Asymmetric 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh....eeeee.hhh........ee.........ee...eeeehhhhh.eeeeeeee..............eeeee...........eeee...eeeeee......eeeeee.........ee..........eee......hhhhhhhhhhhh..eeeee....eeeeee...ee..........ee.hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhh...eeee...........eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeeeee...ee.....eeeeeeee........eeee....hhhhh...eeeee........ee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ers A 319 SPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL 736
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688    || 702       712       722       732    
                                                                                                                                                                                                                                                                                                                                                                                                                693|                                      
                                                                                                                                                                                                                                                                                                                                                                                                                 698
   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 5ERS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
    Leu A:365 - Pro A:366   [ RasMol ]  
    Lys A:602 - Pro A:603   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5ers
    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
  GEPH_RAT | Q03555
    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)
  2.10.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.7.75
    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
  GEPH_RAT | Q03555
    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
        GEPH_RAT | Q03555: 1ihc 1t3e 2fts 2fu3 4pd0 4pd1 4tk1 4tk2 4tk3 4tk4 4u90 4u91 5erq 5err 5ert 5eru 5erv

(-) Related Entries Specified in the PDB File

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