eF-site ID 6ogz-A
PDB Code 6ogz
Chain A

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Title In situ structure of Rotavirus RNA-dependent RNA polymerase at transcript-elongated state
Classification viral protein/rna/transferase
Compound RNA (5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*A)-3')
Source ORGANISM_SCIENTIFIC: Rotavirus A;
Sequence A:  GKYNLILSEYLSFIYNSQSAVQIPIYYSSNSELENRCIEF
HSKCLENSKNGLSLKKLFVEYSDVIENATLLSILSYSYDK
YNAVERKLVKYAKGKPLEADLTVNELDYENNKITSELFPT
AEEYTDLLMDPAILTSLSSNLNAVMFWLEKHENDVAEKLK
IYKRRLDLFTIVASTVNKYGVPRHNAKYRYEYEVMKDKPY
YLVTWANSSIEMLMSVFSHEDYLIARELIVLSYSNRSTLA
KLVSSPMSILVALVDINGTFITNEELELEFSNKYVRAIVP
DQTFDELKQMLDNMRKAGLTDIPKMIQDWLVDCSIEKFPL
MAKIYSWSFHVGFRKQKMLDAALDQLKTEYTEDVDDEMYR
EYTMLIRDEVVKMLEEPVKHDDHLLQDSELAGLLSMSSAS
NGESRQLKFGRKTIFSTKKNMHVMDDMANGRYTPGIIPPV
NVDKPIPLGRRDVPGRRTRIIFILPYEYFIAQHAVVEKML
IYAKHTREYAEFYSQSNQLLSYGDVTRFLSNNSMVLYTDV
SQWDSSQHNTQPFRKGIIMGLDMLANMTNDARVIQTLNLY
KQTQINLMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANS
IANLALIKTVLSRISNKYSFATKIIRVDGDDNYAVLQFNT
EVTKQMVQDVSNDVRETYARMNTKVKALVSTVGIEIAKRY
IAGGKIFFRAGINLLNNEKKGQSTQWDQAAVLYSNYIVNR
LRGFETDREFILTKIMQMTSVAITGSLRLFPSERVLTTNS
TFKVFDSEDFIIEYGTTDDEVYIQRAFMSLSSQKSGIADE
IAASSTFKNYVSRLSEQLLFSKNNIVSRGIALTEKAKLNS
YAPISLEKRRAQISALLTMLQKPVTFKSSKITINDILRDI
KPFFTVNEAHLPIQYQKFMPTLPDNVQYIIQCIGSRTYQI
EDDGSKSAISRLISKYSVYKPSIEELYKVISLHENEIQLY
LISLGIPKIDADTYVGSKIYSQDKYRILESYVYNLLSINY
GCYQLFDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEV
INHAIKNGSWISLFCNYPKSEMIKLWKKMWNITSLRSPYT
NA
Description (1)  RNA-dependent RNA polymerase of rotavirus A, Inner capsid protein VP2/RNA Complex


Functional site

1) chain A
residue 452
type
ligand
sequence R
description binding site for residue UTP A 1101
source : AC1

2) chain A
residue 457
type
ligand
sequence R
description binding site for residue UTP A 1101
source : AC1

3) chain A
residue 460
type
ligand
sequence R
description binding site for residue UTP A 1101
source : AC1

4) chain A
residue 520
type
ligand
sequence D
description binding site for residue UTP A 1101
source : AC1

5) chain A
residue 521
type
ligand
sequence V
description binding site for residue UTP A 1101
source : AC1

6) chain A
residue 522
type
ligand
sequence S
description binding site for residue UTP A 1101
source : AC1

7) chain A
residue 523
type
ligand
sequence Q
description binding site for residue UTP A 1101
source : AC1

8) chain A
residue 524
type
ligand
sequence W
description binding site for residue UTP A 1101
source : AC1

9) chain A
residue 525
type
ligand
sequence D
description binding site for residue UTP A 1101
source : AC1

10) chain A
residue 591
type
ligand
sequence S
description binding site for residue UTP A 1101
source : AC1

11) chain A
residue 596
type
ligand
sequence T
description binding site for residue UTP A 1101
source : AC1

12) chain A
residue 600
type
ligand
sequence N
description binding site for residue UTP A 1101
source : AC1

13) chain A
residue 631
type
ligand
sequence D
description binding site for residue UTP A 1101
source : AC1

14) chain A
residue 632
type
ligand
sequence D
description binding site for residue UTP A 1101
source : AC1

15) chain A
residue 11
type
ligand
sequence Y
description binding site for residue GTP A 1102
source : AC2

16) chain A
residue 83
type
ligand
sequence N
description binding site for residue GTP A 1102
source : AC2

17) chain A
residue 143
type
ligand
sequence N
description binding site for residue GTP A 1102
source : AC2

18) chain A
residue 184
type
ligand
sequence R
description binding site for residue GTP A 1102
source : AC2

19) chain A
residue 185
type
ligand
sequence H
description binding site for residue GTP A 1102
source : AC2

20) chain A
residue 189
type
ligand
sequence Y
description binding site for residue GTP A 1102
source : AC2

21) chain A
residue 749
type
ligand
sequence R
description binding site for residue GTP A 1102
source : AC2

22) chain A
residue 452
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence R
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

23) chain A
residue 457-458
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence RR
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

24) chain A
residue 460
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence R
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

25) chain A
residue 462
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence I
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

26) chain A
residue 520-525
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence DVSQWD
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

27) chain A
residue 591-592
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence SG
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

28) chain A
residue 596
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence T
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

29) chain A
residue 600
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence N
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

30) chain A
residue 631-632
type binding
ligand UTP: URIDINE 5'-TRIPHOSPHATE
sequence DD
description URIDINE 5'-TRIPHOSPHATE binding site
source pdb_hetatom : UTP_6ogz_A_1101

31) chain A
residue 11
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence Y
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

32) chain A
residue 15
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence I
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

33) chain A
residue 80-81
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence DK
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

34) chain A
residue 83
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence N
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

35) chain A
residue 85
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence V
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

36) chain A
residue 137
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence S
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

37) chain A
residue 139-140
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence SS
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

38) chain A
residue 143
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence N
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

39) chain A
residue 184-186
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence RHN
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

40) chain A
residue 189
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence Y
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

41) chain A
residue 738
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence Q
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102

42) chain A
residue 749
type binding
ligand GTP: GUANOSINE-5'-TRIPHOSPHATE
sequence R
description GUANOSINE-5'-TRIPHOSPHATE binding site
source pdb_hetatom : GTP_6ogz_A_1102


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