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

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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 F:  LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSK
APRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTD
AISKIRRLQGNILTPGTIRGDLANDIGENLIHASDSEDSA
VDEISIWFP
Description (1)  Nucleoside diphosphate kinase (E.C.2.7.4.6)


Functional site

1) chain F
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE MG F 165
source : BC7

2) chain F
residue 115
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MG F 165
source : BC7

3) chain F
residue 9
type
ligand
sequence K
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

4) chain F
residue 53
type
ligand
sequence H
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

5) chain F
residue 62
type
ligand
sequence L
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

6) chain F
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

7) chain F
residue 89
type
ligand
sequence Q
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

8) chain F
residue 99
type
ligand
sequence R
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

9) chain F
residue 106
type
ligand
sequence I
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

10) chain F
residue 107
type
ligand
sequence G
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

11) chain F
residue 109
type
ligand
sequence N
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

12) chain F
residue 112
type
ligand
sequence H
description BINDING SITE FOR RESIDUE TYD F 138
source : BC8

13) chain F
residue 91
type
ligand
sequence N
description BINDING SITE FOR RESIDUE PO4 F 139
source : BC9

14) chain F
residue 92
type
ligand
sequence I
description BINDING SITE FOR RESIDUE PO4 F 139
source : BC9

15) chain F
residue 99
type
ligand
sequence R
description BINDING SITE FOR RESIDUE PO4 F 139
source : BC9

16) chain F
residue 109
type
ligand
sequence N
description BINDING SITE FOR RESIDUE PO4 F 139
source : BC9

17) chain F
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 F
residue 9
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence K
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

19) chain F
residue 50
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence Y
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

20) chain F
residue 53
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence H
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

21) chain F
residue 58
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence Y
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

22) chain F
residue 62
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence L
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

23) chain F
residue 86
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence R
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

24) chain F
residue 89
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence Q
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

25) chain F
residue 99
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence R
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

26) chain F
residue 106-107
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence IG
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

27) chain F
residue 109
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence N
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

28) chain F
residue 112
type binding
ligand TYD: THYMIDINE-5'-DIPHOSPHATE
sequence H
description THYMIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : TYD_3fbc_F_138

29) chain F
residue 109
type catalytic
ligand
sequence N
description Annotated By Reference To The Literature 1nsp
source CSA : CSA6

30) chain F
residue 9
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1nsp
source CSA : CSA6

31) chain F
residue 50
type catalytic
ligand
sequence Y
description Annotated By Reference To The Literature 1nsp
source CSA : CSA12

32) chain F
residue 9
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1nsp
source CSA : CSA12


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