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(-) Description

Title :  TERNARY COMPLEX OF GEPHE - ADP - TUNGSTEN 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 :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Moco, Wco, Tungsten Cofactor, Tungsten Cluster, 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
    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 344-762
    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  (7, 16)

Asymmetric Unit (7, 16)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CA1Ligand/IonCALCIUM ION
4MG1Ligand/IonMAGNESIUM ION
5MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6W9Ligand/IonTUNGSTEN ION
7WO41Ligand/IonTUNGSTATE(VI)ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CA-1Ligand/IonCALCIUM ION
4MG-1Ligand/IonMAGNESIUM ION
5MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6W-1Ligand/IonTUNGSTEN ION
7WO42Ligand/IonTUNGSTATE(VI)ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:414 , SER 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 , CA A:814 , HOH A:940 , HOH A:1005 , HOH A:1027 , HOH A:1080 , HOH A:1089 , HOH A:1093 , HOH A:1132 , HOH A:1168 , HOH A:1172binding site for residue ADP A 801
02AC2SOFTWAREASP A:580 , ADP A:801 , HOH A:1001 , HOH A:1027 , HOH A:1168binding site for residue MG A 802
03AC3SOFTWARELYS A:373 , W A:811binding site for residue W A 803
04AC4SOFTWAREW A:807 , W A:809 , W A:810 , W A:811 , WO4 A:816binding site for residue W A 804
05AC5SOFTWAREW A:806 , W A:807 , W A:811binding site for residue W A 805
06AC6SOFTWAREW A:805 , W A:811binding site for residue W A 806
07AC7SOFTWAREW A:804 , W A:805 , W A:808 , W A:809 , W A:811 , WO4 A:816binding site for residue W A 807
08AC8SOFTWAREW A:807 , WO4 A:816 , HOH A:1226binding site for residue W A 808
09AC9SOFTWAREW A:804 , W A:807 , W A:811 , HOH A:1262binding site for residue W A 809
10AD1SOFTWARELEU A:605 , W A:804 , W A:811binding site for residue W A 810
11AD2SOFTWAREW A:803 , W A:804 , W A:805 , W A:806 , W A:807 , W A:809 , W A:810binding site for residue W A 811
12AD3SOFTWARECYS A:469 , SER A:702binding site for residue ACT A 812
13AD4SOFTWAREARG A:564 , ALA A:565 , LYS A:619binding site for residue ACT A 813
14AD5SOFTWAREADP A:801 , HOH A:992 , HOH A:1004 , HOH A:1027 , HOH A:1035 , HOH A:1076 , HOH A:1083binding site for residue CA A 814
15AD6SOFTWAREARG A:348 , ASN A:512 , GLU A:514 , HOH A:1220binding site for residue MPD A 815
16AD7SOFTWAREPRO A:603 , GLY A:604 , LEU A:605 , PRO A:606 , PRO A:625 , ASN A:627 , SER A:630 , W A:804 , W A:807 , W A:808 , HOH A:1005binding site for residue WO4 A 816

(-) SS Bonds  (0, 0)

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

(-) 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 5ERV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERV)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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..hhhhhh...eeeee........ee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erv A 319 SPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL 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   ||  703       713       723       733   
                                                                                                                                                                                                                                                                                                                                                                                                               692|                                      
                                                                                                                                                                                                                                                                                                                                                                                                                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 5ERV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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    Leu A:365 - Pro A:366   [ RasMol ]  
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  5erv
    Family and Domain Information: ProDom | SYSTERS
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  GEPH_RAT | Q03555
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  2.10.1.1
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  2.7.7.75
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
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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 5ert 5eru

(-) Related Entries Specified in the PDB File

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