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(-) Description

Title :  NDPK IN COMPLEX WITH (RP)-SPMPAPP
 
Authors :  S. Priet, F. Ferron, K. Alvarez, M. Verron, B. Canard
Date :  31 Jan 14  (Deposition) - 11 Feb 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Priet, L. Roux, M. Saez-Ayala, F. Ferron, B. Canard, K. Alvarez
Enzymatic Synthesis Of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect Of The Alpha-Phosphorus Configuration On Hiv-1 Rt Activity.
Antiviral Res. V. 117 122 2015
PubMed-ID: 25766862  |  Reference-DOI: 10.1016/J.ANTIVIRAL.2015.03.003

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETG20A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 44689
    Other Details: S-PMPAPP
    Synonym: NDK, NDP KINASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):    DEF
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1EOI6Ligand/Ion[[(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-2-YL]OXYMETHYL-SULFANYL-PHOSPHORYL] PHOSPHONO HYDROGENPHOSPHATE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EOI3Ligand/Ion[[(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-2-YL]OXYMETHYL-SULFANYL-PHOSPHORYL] PHOSPHONO HYDROGENPHOSPHATE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EOI3Ligand/Ion[[(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-2-YL]OXYMETHYL-SULFANYL-PHOSPHORYL] PHOSPHONO HYDROGENPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:16 , HIS A:59 , PHE A:64 , LEU A:68 , ARG A:92 , THR A:98 , ARG A:109 , VAL A:116 , ASN A:119 , HOH A:2082 , HOH A:2090 , HOH A:2097 , HOH A:2101BINDING SITE FOR RESIDUE EOI A1156
2AC2SOFTWARELYS C:16 , HIS C:59 , PHE C:64 , LEU C:68 , ARG C:92 , THR C:98 , ARG C:109 , ASN C:119 , HOH C:2049 , HOH C:2058BINDING SITE FOR RESIDUE EOI C1156
3AC3SOFTWARELYS F:16 , HIS F:59 , PHE F:64 , ARG F:92 , THR F:98 , ARG F:109 , VAL F:116 , ASN F:119 , GLY F:123 , ASP F:125 , HOH F:2025 , HOH F:2039BINDING SITE FOR RESIDUE EOI F1156
4AC4SOFTWARELYS B:16 , HIS B:59 , PHE B:64 , ARG B:92 , THR B:98 , ARG B:109 , VAL B:116 , ASN B:119 , HOH B:2046 , HOH B:2049 , HOH B:2057 , HOH B:2058 , HOH B:2081BINDING SITE FOR RESIDUE EOI B1156
5AC5SOFTWARELYS E:16 , HIS E:59 , PHE E:64 , ARG E:92 , THR E:98 , ARG E:109 , VAL E:116 , ASN E:119 , HOH E:2037 , HOH E:2041 , HOH E:2042 , HOH E:2048 , HOH E:2060 , HOH E:2062BINDING SITE FOR RESIDUE EOI E1156
6AC6SOFTWARELYS D:16 , HIS D:59 , PHE D:64 , LEU D:68 , ARG D:92 , THR D:98 , ARG D:109 , ASN D:119 , HOH D:2012 , HOH D:2042 , HOH D:2074BINDING SITE FOR RESIDUE EOI D1156

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CP5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:5 -Val A:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CP5)

(-) Exons   (0, 0)

(no "Exon" information available for 4CP5)

(-) 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:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp5 A   5 KVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp5 B   5 KVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain C from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp5 C   5 KVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain D from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp5 D   5 KVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain E from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp5 E   5 KVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain F from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp5 F   5 KVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
   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  (0, 0)

(no "SCOP Domain" information available for 4CP5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CP5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CP5)

(-) Gene Ontology  (32, 32)

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  NDKC_DICDI | P22887
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 Related Entries

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

UniProtKB/Swiss-Prot
        NDKC_DICDI | P22887: 1b4s 1b99 1bux 1f3f 1f6t 1hhq 1hiy 1hlw 1kdn 1leo 1lwx 1mn7 1mn9 1ncl 1ndc 1ndk 1ndp 1npk 1nsp 1pae 1s5z 2bef 3fkb 4c6a

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4CP5)