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(-) Description

Title :  ENGINEERED RABGGTASE IN COMPLEX WITH BMS ANALOGUE 12
 
Authors :  Z. Guo, E. A. Stigter, R. S. Bon, H. Waldmann, W. Blankenfeldt, R. S. Good
Date :  29 Aug 12  (Deposition) - 24 Oct 12  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Prenylation, Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Stigter, Z. Guo, R. S. Bon, Y. W. Wu, A. Choidas, A. Wolf, S. Menninger, H. Waldmann, W. Blankenfeldt, R. S. Goody
Development Of Selective, Potent Rabggtase Inhibitors
J. Med. Chem. V. 55 8330 2012
PubMed-ID: 22963166  |  Reference-DOI: 10.1021/JM300624S

(-) Compounds

Molecule 1 - GERANYLGERANYL TRANSFERASE TYPE-2 SUBUNIT ALPHA
    Chains: A
    EC Number: 2.5.1.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGATEV
    Expression System Strain: BL21 CODON-PLUS RIL (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-237 AND 353-441 LINKED WITH AGSG
    Gene: RABGGTA, GGTA
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GERANYLGERANYL TRANSFERASE TYPE II SUBUNIT ALPHA, RAB GERANYL-GERANYLTRANSFERASE SUBUNIT ALPHA, RAB GG TRANSFERASE ALPHA, RAB GGTASE ALPHA, RAB GERANYLGERANYLTRANSFERASE SUBUNIT ALPHA
 
Molecule 2 - GERANYLGERANYL TRANSFERASE TYPE-2 SUBUNIT BETA
    Chains: B
    EC Number: 2.5.1.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET27B
    Expression System Strain: BL21 CODON-PLUS RIL (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RABGGTB, GGTB
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GERANYLGERANYL TRANSFERASE TYPE II SUBUNIT BETA, GGTASE-II- BETA, RAB GERANYL-GERANYLTRANSFERASE SUBUNIT BETA, RAB GG TRANSFERASE BETA, RAB GGTASE BETA, RAB GERANYLGERANYLTRANSFERASE SUBUNIT BETA, TYPE II PROTEIN GERANYL-GERANYLTRANSFERASE SUBUNIT BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
17TQ1Ligand/Ion4-({(3R)-7-CYANO-4-[(4-METHOXYPHENYL)SULFONYL]-1-[(1-METHYL-1H-IMIDAZOL-5-YL)METHYL]-2,3,4,5-TETRAHYDRO-1H-1,4-BENZODIAZEPIN-3-YL}METHYL)PHENYL BENZYLCARBAMATE
2CA1Ligand/IonCALCIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:238 , CYS B:240 , HIS B:290 , 7TQ B:403BINDING SITE FOR RESIDUE ZN B 401
2AC2SOFTWAREALA A:138 , HIS B:64 , MET B:66BINDING SITE FOR RESIDUE CA B 402
3AC3SOFTWAREASP A:61 , TYR B:44 , GLN B:103 , PHE B:147 , TYR B:195 , ASP B:287 , PHE B:289 , ZN B:401 , HOH B:525 , HOH B:559 , HOH B:603 , HOH B:611 , HOH B:641BINDING SITE FOR RESIDUE 7TQ B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GTT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GTT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GTT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GTT)

(-) Exons   (0, 0)

(no "Exon" information available for 4GTT)

(-) Sequences/Alignments

Asymmetric/Biological 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gtt A  14 AEAKRLEREQKLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYA 330
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193 ||    209       219       229       239       249       259       269       279       289       299       309       319       329 
                                                                                                                                                                                                               195|                                                                                                                                
                                                                                                                                                                                                                202                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4gttb_ B: Rab geranylgeranyltransferase, beta subunit                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh..............hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gtt B   5 QKDVTIKSDAPDTLLLEKHADYIASYGSDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLQRVNVQPELVS 331
                                    14        24       |37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327    
                                                      32|                                                                                                                                                                                                                                                                                                       
                                                       36
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GTT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GTT)

(-) Gene Ontology  (11, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  2.5.1.60
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PGTA_RAT | Q08602: 1dce 1ltx 3c72 3dss 3dst 3dsu 3dsv 3dsw 3dsx 3hxb 3hxc 3hxd 3hxe 3hxf 3pz1 3pz2 3pz3 4ehm 4gts 4gtv
        PGTB2_RAT | Q08603: 1dce 1ltx 3c72 3dss 3dst 3dsu 3dsv 3dsw 3dsx 3hxb 3hxc 3hxd 3hxe 3hxf 3pz1 3pz2 3pz3 4ehm 4gts 4gtv

(-) Related Entries Specified in the PDB File

4gtm 4gto 4gtp 4gtq 4gtr 4gts 4gtv