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(-) Description

Title :  GEPHE IN COMPLEX WITH MG(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 :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Molybdenum And Tungsten Cofactor, Moco, Wco, Terminal Step, 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, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 22)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4MPD10Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO42Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER 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 , PRO A:628 , MG A:802 , MG A:803 , HOH A:927 , HOH A:990 , HOH A:1060 , HOH A:1096 , HOH A:1104 , HOH A:1105 , HOH A:1131 , HOH A:1141 , HOH A:1196 , HOH A:1202binding site for residue ADP A 801
02AC2SOFTWAREADP A:801 , HOH A:981 , HOH A:990 , HOH A:1060 , HOH A:1141 , HOH A:1202binding site for residue MG A 802
03AC3SOFTWARESER A:575 , ASP A:580 , ADP A:801binding site for residue MG A 803
04AC4SOFTWAREMET A:326 , MET A:711 , HOH A:982 , HOH A:1345binding site for residue ACT A 804
05AC5SOFTWARELEU A:323binding site for residue ACT A 805
06AC6SOFTWARESER A:662 , CYS A:663 , ALA A:689 , SER A:691binding site for residue ACT A 806
07AC7SOFTWAREMET A:336 , THR A:337 , HOH A:1116binding site for residue ACT A 807
08AC8SOFTWAREHIS A:476 , ARG A:644 , THR A:655 , HOH A:913 , HOH A:1181binding site for residue MPD A 808
09AC9SOFTWARECYS A:469 , VAL A:470 , LEU A:471 , ALA A:472binding site for residue MPD A 809
10AD1SOFTWAREGLU A:514 , HOH A:911binding site for residue MPD A 810
11AD2SOFTWARESER A:525 , ARG A:675 , HOH A:942 , HOH A:1242 , HOH A:1361binding site for residue MPD A 811
12AD3SOFTWAREGLY A:604 , LEU A:605 , ARG A:670 , HOH A:1268 , HOH A:1290binding site for residue MPD A 812
13AD4SOFTWAREVAL A:500 , ASP A:566 , LYS A:619 , HOH A:906binding site for residue PO4 A 813

(-) SS Bonds  (0, 0)

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

(-) 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 5ERR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERR)

(-) 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 ....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............eeeee........ee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5err 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)
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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 5ERR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu A:365 - Pro A:366   [ RasMol ]  
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  5err
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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 5ers 5ert 5eru 5erv

(-) Related Entries Specified in the PDB File

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