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(-) Description

Title :  TERNARY COMPLEX OF GEPHE - ADP - MOLYBDENUM CLUSTER
 
Authors :  V. B. Kasaragod, H. Schindelin
Date :  15 Nov 15  (Deposition) - 04 May 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Molybdenum Cluster, Moco, Wco, Moco Biosynthesis, Ternary Complex, 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
    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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 21)

Asymmetric Unit (8, 21)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CA1Ligand/IonCALCIUM ION
4MG1Ligand/IonMAGNESIUM ION
5MO8Ligand/IonMOLYBDENUM ATOM
6MOO1Ligand/IonMOLYBDATE ION
7MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
8PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (5, 22)
No.NameCountTypeFull Name
1ACT10Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CA-1Ligand/IonCALCIUM ION
4MG-1Ligand/IonMAGNESIUM ION
5MO-1Ligand/IonMOLYBDENUM ATOM
6MOO2Ligand/IonMOLYBDATE ION
7MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
8PO42Ligand/IonPHOSPHATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:469binding site for residue ACT A 801
02AC2SOFTWAREALA A:356 , HOH A:1179binding site for residue ACT A 802
03AC3SOFTWAREHOH A:1074 , HOH A:1118binding site for residue ACT A 803
04AC4SOFTWAREMPD A:808 , HOH A:916binding site for residue ACT A 805
05AC5SOFTWAREMET A:326 , ASP A:327 , PHE A:330 , PRO A:654 , ILE A:656 , MET A:731 , HOH A:939binding site for residue MPD A 806
06AC6SOFTWAREASN A:512 , GLU A:514 , HOH A:904 , HOH A:1190 , HOH A:1252binding site for residue MPD A 807
07AC7SOFTWAREARG A:675 , ACT A:805 , HOH A:928 , HOH A:977binding site for residue MPD A 808
08AC8SOFTWAREADP A:810 , HOH A:932 , HOH A:984 , HOH A:1012 , HOH A:1053 , HOH A:1071 , HOH A:1121binding site for residue CA A 809
09AC9SOFTWARESER 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 , CA A:809 , MG A:821 , HOH A:932 , HOH A:972 , HOH A:1026 , HOH A:1077 , HOH A:1081 , HOH A:1111 , HOH A:1122 , HOH A:1149binding site for residue ADP A 810
10AD1SOFTWAREARG A:564 , LYS A:619 , HOH A:910binding site for residue PO4 A 811
11AD2SOFTWAREARG A:670 , MO A:813 , MO A:814 , MO A:816 , MO A:817 , MO A:819 , MOO A:820 , HOH A:1123binding site for residue MO A 812
12AD3SOFTWARELEU A:605 , MO A:812 , MO A:814 , MO A:816binding site for residue MO A 813
13AD4SOFTWAREMO A:812 , MO A:813 , MO A:819 , MOO A:820 , HOH A:1219binding site for residue MO A 814
14AD5SOFTWAREMO A:817 , MO A:818 , MO A:819 , MOO A:820binding site for residue MO A 815
15AD6SOFTWAREMO A:812 , MO A:813 , MO A:817 , MO A:819 , HOH A:1123binding site for residue MO A 816
16AD7SOFTWARELYS A:602 , MO A:812 , MO A:815 , MO A:816 , MOO A:820 , HOH A:1123binding site for residue MO A 817
17AD8SOFTWAREMO A:815 , MO A:819binding site for residue MO A 818
18AD9SOFTWAREMO A:812 , MO A:814 , MO A:815 , MO A:816 , MO A:818binding site for residue MO A 819
19AE1SOFTWAREGLY A:604 , LEU A:605 , PRO A:606 , PRO A:625 , ASN A:627 , SER A:630 , MO A:812 , MO A:814 , MO A:815 , MO A:817 , HOH A:972binding site for residue MOO A 820
20AE2SOFTWAREASP A:580 , ADP A:810 , HOH A:932 , HOH A:1026binding site for residue MG A 821

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 4)

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 5ERU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERU)

(-) 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...hhhhh....eeeee........ee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5eru 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 5ERU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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        GEPH_RAT | Q03555: 1ihc 1t3e 2fts 2fu3 4pd0 4pd1 4tk1 4tk2 4tk3 4tk4 4u90 4u91 5erq 5err 5ers 5ert 5erv

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