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(-) Description

Title :  STRUCTURE OF LEISHMANIA NDKB COMPLEXED WITH AMP.
 
Authors :  D. M. Trindade, T. A. C. B. Sousa, C. C. C. Tonoli, C. R. Santos, R. K. Arni, A. H. C. Oliveira, M. T. Murakami
Date :  13 Jun 10  (Deposition) - 27 Apr 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1:  B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  C,F  (1x)
Biol. Unit 5:  D,E  (1x)
Biol. Unit 6:  G,H  (1x)
Biol. Unit 7:  I,L  (1x)
Biol. Unit 8:  M,N  (1x)
Keywords :  Lmndkb, Amp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Souza, D. M. Trindade, C. C. Tonoli, C. R. Santos, R. J. Ward, R. K. Arni, A. H. Oliveira, M. T. Murakami
Molecular Adaptability Of Nucleoside Diphosphate Kinase B From Trypanosomatid Parasites: Stability, Oligomerization And Structural Determinants Of Nucleotide Binding.
Mol Biosyst V. 7 2189 2011
PubMed-ID: 21528129  |  Reference-DOI: 10.1039/C0MB00307G

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    ChainsA, B, C, D, E, F, G, H, I, J, K, L, M, N
    EC Number2.7.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneL1648.07, LMJF32.2950, NDKB
    Organism ScientificLEISHMANIA MAJOR
    Organism Taxid5664

 Structural Features

(-) Chains, Units

  1234567891011121314
Asymmetric Unit ABCDEFGHIJKLMN
Biological Unit 1 (1x) BCDEF        
Biological Unit 2 (1x)      GHIJKL  
Biological Unit 3 (1x)AB            
Biological Unit 4 (1x)  C  F        
Biological Unit 5 (1x)   DE         
Biological Unit 6 (1x)      GH      
Biological Unit 7 (1x)        I  L  
Biological Unit 8 (1x)            MN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric Unit (1, 13)
No.NameCountTypeFull Name
1AMP13Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1AMP5Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1AMP5Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 6 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 7 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 8 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:11 , TYR A:51 , LEU A:54 , PHE A:59 , LEU A:63 , THR A:93 , VAL A:111 , ASN A:114 , HIS A:117 , HOH A:167 , HOH A:197 , HOH A:273BINDING SITE FOR RESIDUE AMP A 152
02AC2SOFTWARELYS B:11 , TYR B:51 , PHE B:59 , THR B:93 , VAL B:111 , ASN B:114 , HIS B:117 , HOH B:306 , GLU F:151BINDING SITE FOR RESIDUE AMP B 152
03AC3SOFTWAREGLU A:151 , LYS C:11 , TYR C:51 , LEU C:54 , PHE C:59 , THR C:93 , ARG C:104 , VAL C:111 , ASN C:114 , HIS C:117BINDING SITE FOR RESIDUE AMP C 152
04AC4SOFTWARELYS D:11 , TYR D:51 , PHE D:59 , VAL D:111 , ASN D:114 , HIS D:117BINDING SITE FOR RESIDUE AMP D 152
05AC5SOFTWARELYS E:11 , TYR E:51 , LEU E:54 , PHE E:59 , VAL E:111 , ASN E:114 , HIS E:117BINDING SITE FOR RESIDUE AMP E 152
06AC6SOFTWAREGLU D:151 , LYS F:11 , TYR F:51 , PHE F:59 , ARG F:104 , VAL F:111 , HIS F:117 , HOH F:301BINDING SITE FOR RESIDUE AMP F 152
07AC7SOFTWARELYS G:11 , TYR G:51 , PHE G:59 , LEU G:63 , THR G:93 , VAL G:111 , ASN G:114 , HIS G:117 , GLU K:151BINDING SITE FOR RESIDUE AMP G 152
08AC8SOFTWARELYS H:11 , TYR H:51 , PHE H:59 , VAL H:111 , ASN H:114 , HIS H:117 , HOH H:158 , HOH H:205BINDING SITE FOR RESIDUE AMP H 152
09AC9SOFTWARELYS I:11 , TYR I:51 , PHE I:59 , LEU I:63 , THR I:93 , VAL I:111 , ASN I:114 , HIS I:117BINDING SITE FOR RESIDUE AMP I 152
10BC1SOFTWAREGLU H:151 , LYS J:11 , TYR J:51 , LEU J:54 , PHE J:59 , THR J:93 , ARG J:104 , VAL J:111 , HIS J:117 , HOH J:156BINDING SITE FOR RESIDUE AMP J 152
11BC2SOFTWARELYS K:11 , TYR K:51 , PHE K:59 , LEU K:63 , THR K:93 , ASN K:114 , HIS K:117BINDING SITE FOR RESIDUE AMP K 152
12BC3SOFTWARELYS M:11 , TYR M:51 , LEU M:54 , PHE M:59 , THR M:93 , ARG M:104 , VAL M:111 , ASN M:114 , HIS M:117 , GLU M:151 , HOH M:211BINDING SITE FOR RESIDUE AMP M 152
13BC4SOFTWARELYS N:11 , TYR N:51 , LEU N:54 , PHE N:59 , THR N:93 , VAL N:111 , ASN N:114 , HIS N:117 , GLU N:151 , HOH N:159 , HOH N:162BINDING SITE FOR RESIDUE AMP N 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NGT)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:2 -Ser A:3
2Ser D:2 -Ser D:3
3Ser F:3 -Glu F:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NGT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NGT)

(-) Exons   (0, 0)

(no "Exon" information available for 3NGT)

(-) 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:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngta_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngt A   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:148
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143        
         Q9U1E1_LEIMA     4 ERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtb_ B: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh.hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt B   4 ERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143        

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:148
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143        
         Q9U1E1_LEIMA     4 ERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtc_ C: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt C   4 ERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143        

Chain D from PDB  Type:PROTEIN  Length:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtd_ D: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngt D   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain E from PDB  Type:PROTEIN  Length:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngte_ E: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee....hhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngt E   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain F from PDB  Type:PROTEIN  Length:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtf_ F: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngt F   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain G from PDB  Type:PROTEIN  Length:149
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
         Q9U1E1_LEIMA     3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtg_ G: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh....hhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt G   3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain H from PDB  Type:PROTEIN  Length:147
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
         Q9U1E1_LEIMA     3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngth_ H: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhh...--...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt H   3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKD--SKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    12        22        32        42        52|  |    62        72        82        92       102       112       122       132       142         
                                                                             53 56                                                                                               

Chain I from PDB  Type:PROTEIN  Length:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngti_ I: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhh....eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngt I   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain J from PDB  Type:PROTEIN  Length:148
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q9U1E1_LEIMA     3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIY 150
               SCOP domains d3ngtj_ J: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh..ee..hhhhhhhhhhhhhhhhhh......hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt J   3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIY 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        

Chain K from PDB  Type:PROTEIN  Length:149
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
         Q9U1E1_LEIMA     3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtk_ K: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt K   3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain L from PDB  Type:PROTEIN  Length:125
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIY 150
               SCOP domains d3ngtl_ L: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..------------------------.....eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee...hhhhhhhhhhhhhhhhh......hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt L   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQP------------------------FSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIY 150
                                    11        21        31        41|        -         -     |  71        81        91       101       111       121       131       141         
                                                                   42                       67                                                                                   

Chain M from PDB  Type:PROTEIN  Length:149
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
         Q9U1E1_LEIMA     3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtm_ M: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngt M   3 SERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain N from PDB  Type:PROTEIN  Length:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngtn_ N: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --NDK-3ngtN01 N:4-138                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) --NDK-3ngtN02 N:4-138                                                                                                                    ------------- Pfam domains (2)
           Pfam domains (3) --NDK-3ngtN03 N:4-138                                                                                                                    ------------- Pfam domains (3)
           Pfam domains (4) --NDK-3ngtN04 N:4-138                                                                                                                    ------------- Pfam domains (4)
           Pfam domains (5) --NDK-3ngtN05 N:4-138                                                                                                                    ------------- Pfam domains (5)
           Pfam domains (6) --NDK-3ngtN06 N:4-138                                                                                                                    ------------- Pfam domains (6)
           Pfam domains (7) --NDK-3ngtN07 N:4-138                                                                                                                    ------------- Pfam domains (7)
           Pfam domains (8) --NDK-3ngtN08 N:4-138                                                                                                                    ------------- Pfam domains (8)
           Pfam domains (9) --NDK-3ngtN09 N:4-138                                                                                                                    ------------- Pfam domains (9)
          Pfam domains (10) --NDK-3ngtN10 N:4-138                                                                                                                    ------------- Pfam domains (10)
          Pfam domains (11) --NDK-3ngtN11 N:4-138                                                                                                                    ------------- Pfam domains (11)
          Pfam domains (12) --NDK-3ngtN12 N:4-138                                                                                                                    ------------- Pfam domains (12)
          Pfam domains (13) --NDK-3ngtN13 N:4-138                                                                                                                    ------------- Pfam domains (13)
          Pfam domains (14) --NDK-3ngtN14 N:4-138                                                                                                                    ------------- Pfam domains (14)
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhh.......hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngt N   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

   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, 14)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NGT)

(-) Pfam Domains  (1, 14)

Asymmetric Unit
(-)
Family: NDK (40)
1aNDK-3ngtN01N:4-138
1bNDK-3ngtN02N:4-138
1cNDK-3ngtN03N:4-138
1dNDK-3ngtN04N:4-138
1eNDK-3ngtN05N:4-138
1fNDK-3ngtN06N:4-138
1gNDK-3ngtN07N:4-138
1hNDK-3ngtN08N:4-138
1iNDK-3ngtN09N:4-138
1jNDK-3ngtN10N:4-138
1kNDK-3ngtN11N:4-138
1lNDK-3ngtN12N:4-138
1mNDK-3ngtN13N:4-138
1nNDK-3ngtN14N:4-138

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L,M,N   (Q9U1E1_LEIMA | Q9U1E1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0006183    GTP biosynthetic process    The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
    GO:0006228    UTP biosynthetic process    The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0009142    nucleoside triphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9U1E1_LEIMA | Q9U1E13ngr 3ngs 3ngu 5c7p 5caa 5cab

(-) Related Entries Specified in the PDB File

3ngr THE SAME PROTEIN WITH UNORDERED NUCLEOTIDE-BINDING LOOP
3ngs THE SAME PROTEIN WITH ORDERED NUCLEOTIDE-BINDING LOOP
3ngu THE SAME PROTEIN COMPLEXED WITH ADP.