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(-) Description

Title :  GEPHE IN COMPLEX WITH MN(2+) - ADP
 
Authors :  V. B. Kasaragod, H. Schindelin
Date :  15 Nov 15  (Deposition) - 04 May 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Moco, Wco, Moco Biosyntheis, Adp Complex, Manganese, 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
    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
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MN2Ligand/IonMANGANESE (II) ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MN-1Ligand/IonMANGANESE (II) ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO44Ligand/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 , VAL A:574 , SER A:575 , ASP A:580 , PRO A:625 , GLY A:626 , ASN A:627 , MN A:802 , MN A:803 , HOH A:946 , HOH A:994 , HOH A:1002 , HOH A:1015binding site for residue ADP A 801
2AC2SOFTWAREADP A:801 , HOH A:930 , HOH A:945 , HOH A:964 , HOH A:1026 , HOH A:1157binding site for residue MN A 802
3AC3SOFTWAREASP A:580 , ADP A:801binding site for residue MN A 803
4AC4SOFTWARELEU A:736 , HOH A:903binding site for residue PO4 A 804
5AC5SOFTWAREASP A:566 , LYS A:619binding site for residue PO4 A 805
6AC6SOFTWARELEU A:323 , PHE A:600binding site for residue ACT A 806
7AC7SOFTWAREMET A:711 , HOH A:985binding site for residue ACT A 807
8AC8SOFTWAREMET A:336binding site for residue ACT A 808
9AC9SOFTWAREPRO A:628 , ARG A:675 , HOH A:947binding site for residue MPD A 809

(-) SS Bonds  (0, 0)

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

(-) 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 5ERT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERT)

(-) 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:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               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
                 5ert A 319 SPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL 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     ||701       711       721       731     
                                                                                                                                                                                                                                                                                                                                                                                                                 694|                                      
                                                                                                                                                                                                                                                                                                                                                                                                                  698
   Legend:   → Mismatch (orange background)
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  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 5ERT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu A:365 - Pro A:366   [ RasMol ]  
    Lys A:602 - Pro A:603   [ RasMol ]  
    Ser A:319 - Pro A:320   [ RasMol ]  
 
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  5ert
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  GEPH_RAT | Q03555
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  2.10.1.1
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  2.7.7.75
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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 5erq 5err 5ers 5eru 5erv

(-) Related Entries Specified in the PDB File

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