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

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


Functional site

1) chain D
residue 115
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MG D 202
source : AC7

2) chain D
residue 9
type
ligand
sequence K
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

3) chain D
residue 53
type
ligand
sequence H
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

4) chain D
residue 58
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

5) chain D
residue 62
type
ligand
sequence L
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

6) chain D
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

7) chain D
residue 99
type
ligand
sequence R
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

8) chain D
residue 106
type
ligand
sequence I
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

9) chain D
residue 107
type
ligand
sequence G
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

10) chain D
residue 109
type
ligand
sequence N
description BINDING SITE FOR RESIDUE UDP D 201
source : AC8

11) chain D
residue 117
type ACT_SITE
ligand
sequence E
description Pros-phosphohistidine intermediate (By similarity).
source Swiss-Prot : SWS_FT_FI7

12) chain D
residue 14
type BINDING
ligand
sequence E
description ATP.
source Swiss-Prot : SWS_FT_FI8

13) chain D
residue 63
type BINDING
ligand
sequence C
description ATP.
source Swiss-Prot : SWS_FT_FI8

14) chain D
residue 91
type BINDING
ligand
sequence N
description ATP.
source Swiss-Prot : SWS_FT_FI8

15) chain D
residue 104
type BINDING
ligand
sequence N
description ATP.
source Swiss-Prot : SWS_FT_FI8

16) chain D
residue 114
type BINDING
ligand
sequence S
description ATP.
source Swiss-Prot : SWS_FT_FI8

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 UDP: URIDINE-5'-DIPHOSPHATE
sequence K
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

19) chain D
residue 50
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence Y
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

20) chain D
residue 53
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence H
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

21) chain D
residue 58
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence Y
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

22) chain D
residue 62
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence L
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

23) chain D
residue 86
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence R
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

24) chain D
residue 89
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence Q
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

25) chain D
residue 99
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence R
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

26) chain D
residue 106-109
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence IGEN
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

27) chain D
residue 111-112
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence IH
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_D_201

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

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

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

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


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