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(-) Description

Title :  GEPHYRIN E DOMAIN AT 1.55 ANGSTROM RESOLUTION
 
Authors :  V. B. Kasaragod, H. Schindelin
Date :  15 Nov 15  (Deposition) - 04 May 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Molybdenum Cofactor, Tungsten Cofactor, Moco Biosynthesis, 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  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1ACT10Ligand/IonACETATE ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1ACT20Ligand/IonACETATE ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:600binding site for residue ACT A 801
02AC2SOFTWARECYS A:469 , VAL A:470 , SER A:702binding site for residue ACT A 802
03AC3SOFTWAREHOH A:950binding site for residue ACT A 803
04AC4SOFTWAREARG A:564 , ASP A:566 , LYS A:619 , HOH A:1019binding site for residue ACT A 804
05AC5SOFTWAREMET A:336 , HOH A:1100 , HOH A:1123 , HOH A:1232binding site for residue ACT A 805
06AC6SOFTWAREHOH A:1192binding site for residue ACT A 806
07AC7SOFTWAREASP A:613 , GLY A:616binding site for residue ACT A 807
08AC8SOFTWAREMPD A:811 , HOH A:906 , HOH A:974binding site for residue ACT A 808
09AC9SOFTWAREGLU A:672 , HIS A:674 , HOH A:913 , HOH A:1208binding site for residue ACT A 809
10AD1SOFTWARESER A:480 , PRO A:628 , ARG A:675 , ACT A:808 , HOH A:1040 , HOH A:1070binding site for residue MPD A 811
11AD2SOFTWAREILE A:417 , PRO A:418 , ALA A:421 , HOH A:1065binding site for residue MPD A 812

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:319 -Pro A:320
2Leu A:365 -Pro A:366
3Lys A:602 -Pro A:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERQ)

(-) 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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhhhhhh....eeeee.hhh........ee.........ee...eeeehhhhh.eeeeeeeee.............eeeee...........eeee...eeeeee......eeeeee.........ee..........eee......hhhhhhhhhhhh..eeeee....eeeeee...ee..........ee.hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhh...eeee.ee........eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeeeee...ee.....eeeeeeee........eeee.....hhhhh....eeeee........ee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erq A 318 MSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL 736
                                   327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       699       709       719       729       
                                                                                                                                                                                                                                                                                                                                                                                                                   695|                                      
                                                                                                                                                                                                                                                                                                                                                                                                                    698
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5ERQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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  GEPH_RAT | Q03555
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 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 5err 5ers 5ert 5eru 5erv

(-) Related Entries Specified in the PDB File

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