eF-site ID 3fbc-D
PDB Code 3fbc
Chain D

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Title Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with dTDP
Classification TRANSFERASE
Compound Nucleoside diphosphate kinase
Source (NDK_MIMIV)
Sequence D:  GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWS
KAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGT
DAISKIRRLQGNILTPGTIRGDLANDIGENLIHASDSEDS
AVDEISIWFPE
Description (1)  Nucleoside diphosphate kinase (E.C.2.7.4.6)


Functional site

1) chain D
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE MG D 163
source : BC1

2) chain D
residue 115
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MG D 163
source : BC1

3) chain D
residue 9
type
ligand
sequence K
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

4) chain D
residue 53
type
ligand
sequence H
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

5) chain D
residue 58
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

6) chain D
residue 62
type
ligand
sequence L
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

7) chain D
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

8) chain D
residue 99
type
ligand
sequence R
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

9) chain D
residue 106
type
ligand
sequence I
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

10) chain D
residue 107
type
ligand
sequence G
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

11) chain D
residue 109
type
ligand
sequence N
description BINDING SITE FOR RESIDUE TYD D 138
source : BC2

12) chain D
residue 91
type
ligand
sequence N
description BINDING SITE FOR RESIDUE PO4 D 139
source : BC3

13) chain D
residue 92
type
ligand
sequence I
description BINDING SITE FOR RESIDUE PO4 D 139
source : BC3

14) chain D
residue 99
type
ligand
sequence R
description BINDING SITE FOR RESIDUE PO4 D 139
source : BC3

15) chain D
residue 106
type
ligand
sequence I
description BINDING SITE FOR RESIDUE PO4 D 139
source : BC3

16) chain D
residue 109
type
ligand
sequence N
description BINDING SITE FOR RESIDUE PO4 D 139
source : BC3

17) chain D
residue 109-117
type prosite
ligand
sequence NLIHASDSE
description Nucleoside diphosphate kinases active site. N-x(2)-H-[GA]-S-D-[GSA]-[LIVMPKNE]
source prosite : PS00469

18) chain D
residue 9
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence K
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

19) chain D
residue 50
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence Y
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

20) chain D
residue 53
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence H
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

21) chain D
residue 58
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence Y
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

22) chain D
residue 62
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence L
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

23) chain D
residue 86
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence R
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

24) chain D
residue 89
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence Q
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

25) chain D
residue 99
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence R
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

26) chain D
residue 106-107
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence IG
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

27) chain D
residue 109
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence N
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

28) chain D
residue 112
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence H
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

29) chain D
residue 115
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence D
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_D_138

30) chain D
residue 109
type catalytic
ligand
sequence N
description Annotated By Reference To The Literature 1nsp
source CSA : CSA4

31) chain D
residue 9
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1nsp
source CSA : CSA4

32) chain D
residue 50
type catalytic
ligand
sequence Y
description Annotated By Reference To The Literature 1nsp
source CSA : CSA10

33) chain D
residue 9
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1nsp
source CSA : CSA10


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