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

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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 A:  AGLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFW
SKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEG
TDAISKIRRLQGNILTPGTIRGDLANDIGENLIHASDSED
SAVDEISIWFPET
Description (1)  Nucleoside diphosphate kinase (E.C.2.7.4.6)


Functional site

1) chain A
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE MG A 202
source : AC1

2) chain A
residue 115
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MG A 202
source : AC1

3) chain A
residue 9
type
ligand
sequence K
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

4) chain A
residue 53
type
ligand
sequence H
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

5) chain A
residue 58
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

6) chain A
residue 62
type
ligand
sequence L
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

7) chain A
residue 86
type
ligand
sequence R
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

8) chain A
residue 89
type
ligand
sequence Q
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

9) chain A
residue 99
type
ligand
sequence R
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

10) chain A
residue 106
type
ligand
sequence I
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

11) chain A
residue 107
type
ligand
sequence G
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

12) chain A
residue 109
type
ligand
sequence N
description BINDING SITE FOR RESIDUE UDP A 201
source : AC2

13) chain A
residue 117
type ACT_SITE
ligand
sequence E
description Pros-phosphohistidine intermediate (By similarity).
source Swiss-Prot : SWS_FT_FI1

14) chain A
residue 14
type BINDING
ligand
sequence E
description ATP.
source Swiss-Prot : SWS_FT_FI2

15) chain A
residue 63
type BINDING
ligand
sequence C
description ATP.
source Swiss-Prot : SWS_FT_FI2

16) chain A
residue 91
type BINDING
ligand
sequence N
description ATP.
source Swiss-Prot : SWS_FT_FI2

17) chain A
residue 104
type BINDING
ligand
sequence N
description ATP.
source Swiss-Prot : SWS_FT_FI2

18) chain A
residue 114
type BINDING
ligand
sequence S
description ATP.
source Swiss-Prot : SWS_FT_FI2

19) chain A
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

20) chain A
residue 9
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence K
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

21) chain A
residue 50
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence Y
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

22) chain A
residue 53
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence H
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

23) chain A
residue 58
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence Y
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

24) chain A
residue 62
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence L
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

25) chain A
residue 86
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence R
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

26) chain A
residue 89
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence Q
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

27) chain A
residue 99
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence R
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

28) chain A
residue 106-109
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence IGEN
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

29) chain A
residue 111-112
type binding
ligand UDP: URIDINE-5'-DIPHOSPHATE
sequence IH
description URIDINE-5'-DIPHOSPHATE binding site
source pdb_hetatom : UDP_3fbb_A_201

30) chain A
residue 109
type catalytic
ligand
sequence N
description Annotated By Reference To The Literature 1nsp
source CSA : CSA1

31) chain A
residue 9
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1nsp
source CSA : CSA1

32) chain A
residue 50
type catalytic
ligand
sequence Y
description Annotated By Reference To The Literature 1nsp
source CSA : CSA7

33) chain A
residue 9
type catalytic
ligand
sequence K
description Annotated By Reference To The Literature 1nsp
source CSA : CSA7


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