eF-site ID 5npp-D
PDB Code 5npp
Chain D

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Title 2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA
Classification ISOMERASE
Compound DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
Source Staphylococcus aureus (strain N315) (5NPP)
Sequence D:  GKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAIL
PLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDL
AKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAG
YVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLE
DAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMR
ESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMT
PDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSY
RYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDI
NKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGM
ATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFP
TAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRI
VVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLR
TGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALV
NGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAH
ILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSE
KQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETIL
ADEEVLLQLVRDELTEIRDRFGDDRRTEIQL
Description (1)  DNA gyrase subunit B, DNA gyrase subunit A/DNA Complex


Functional site

1) chain D
residue 1315
type
ligand
sequence S
description binding site for residue GOL B 1503
source : AC3

2) chain D
residue 1319
type
ligand
sequence N
description binding site for residue GOL B 1503
source : AC3

3) chain D
residue 508
type
ligand
sequence D
description binding site for residue MN D 1501
source : AC8

4) chain D
residue 510
type
ligand
sequence D
description binding site for residue MN D 1501
source : AC8

5) chain D
residue 630
type
ligand
sequence R
description binding site for residue 94K D 1502
source : AC9

6) chain D
residue 633
type
ligand
sequence I
description binding site for residue 94K D 1502
source : AC9

7) chain D
residue 634
type
ligand
sequence E
description binding site for residue 94K D 1502
source : AC9

8) chain D
residue 637
type
ligand
sequence A
description binding site for residue 94K D 1502
source : AC9

9) chain D
residue 1031
type
ligand
sequence V
description binding site for residue 94K D 1502
source : AC9

10) chain D
residue 1179
type
ligand
sequence M
description binding site for residue 94K D 1502
source : AC9

11) chain D
residue 1342
type
ligand
sequence R
description binding site for residue 94K D 1502
source : AC9

12) chain D
residue 1343
type
ligand
sequence P
description binding site for residue 94K D 1502
source : AC9

13) chain D
residue 1044
type
ligand
sequence P
description binding site for residue GOL D 1503
source : AD1

14) chain D
residue 1047
type
ligand
sequence R
description binding site for residue GOL D 1503
source : AD1

15) chain D
residue 1156
type
ligand
sequence E
description binding site for residue GOL D 1503
source : AD1

16) chain D
residue 1251
type
ligand
sequence E
description binding site for residue GOL D 1504
source : AD2

17) chain D
residue 1255
type
ligand
sequence G
description binding site for residue GOL D 1504
source : AD2

18) chain D
residue 1256
type
ligand
sequence R
description binding site for residue GOL D 1504
source : AD2

19) chain D
residue 1257
type
ligand
sequence Q
description binding site for residue GOL D 1504
source : AD2

20) chain D
residue 1115
type
ligand
sequence G
description binding site for residue GOL D 1505
source : AD3

21) chain D
residue 1267
type
ligand
sequence Q
description binding site for residue GOL D 1505
source : AD3

22) chain D
residue 1389
type
ligand
sequence D
description binding site for residue GOL D 1506
source : AD4

23) chain D
residue 1390
type
ligand
sequence H
description binding site for residue GOL D 1506
source : AD4

24) chain D
residue 1068
type
ligand
sequence A
description binding site for residue 6EJ C 101
source : AD6

25) chain D
residue 1075
type
ligand
sequence M
description binding site for residue 6EJ C 101
source : AD6

26) chain D
residue 1083
type
ligand
sequence D
description binding site for residue 6EJ C 101
source : AD6

27) chain D
residue 1121
type
ligand
sequence M
description binding site for residue 6EJ C 101
source : AD6

28) chain D
residue 1084
type
ligand
sequence S
description binding site for residue GOL C 102
source : AD7

29) chain D
residue 1068
type binding
ligand 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
sequence A
description (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one binding site
source pdb_hetatom : 6EJ_5npp_C_101

30) chain D
residue 1071-1072
type binding
ligand 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
sequence VG
description (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one binding site
source pdb_hetatom : 6EJ_5npp_C_101

31) chain D
residue 1075
type binding
ligand 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
sequence M
description (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one binding site
source pdb_hetatom : 6EJ_5npp_C_101

32) chain D
residue 1083
type binding
ligand 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
sequence D
description (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one binding site
source pdb_hetatom : 6EJ_5npp_C_101

33) chain D
residue 1121
type binding
ligand 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
sequence M
description (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one binding site
source pdb_hetatom : 6EJ_5npp_C_101

34) chain D
residue 630
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence R
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

35) chain D
residue 633-634
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence IE
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

36) chain D
residue 637-639
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence AVY
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

37) chain D
residue 1027
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence M
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

38) chain D
residue 1030-1031
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence IV
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

39) chain D
residue 1179
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence M
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

40) chain D
residue 1336
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence I
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

41) chain D
residue 1341-1345
type binding
ligand 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
sequence GRPKL
description ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide binding site
source pdb_hetatom : 94K_5npp_D_1502

42) chain D
residue 1031-1032
type binding
ligand GOL: GLYCEROL
sequence VA
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1503

43) chain D
residue 1044
type binding
ligand GOL: GLYCEROL
sequence P
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1503

44) chain D
residue 1047-1048
type binding
ligand GOL: GLYCEROL
sequence RR
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1503

45) chain D
residue 1147
type binding
ligand GOL: GLYCEROL
sequence I
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1503

46) chain D
residue 1156-1158
type binding
ligand GOL: GLYCEROL
sequence EPS
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1503

47) chain D
residue 1084-1085
type binding
ligand GOL: GLYCEROL
sequence SS
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_C_102

48) chain D
residue 1097
type binding
ligand GOL: GLYCEROL
sequence F
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1505

49) chain D
residue 1112-1115
type binding
ligand GOL: GLYCEROL
sequence SMDG
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1505

50) chain D
residue 1267-1269
type binding
ligand GOL: GLYCEROL
sequence QVN
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1505

51) chain D
residue 1251
type binding
ligand GOL: GLYCEROL
sequence E
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1504

52) chain D
residue 1255-1257
type binding
ligand GOL: GLYCEROL
sequence GRQ
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1504

53) chain D
residue 1386
type binding
ligand GOL: GLYCEROL
sequence I
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1506

54) chain D
residue 1389-1390
type binding
ligand GOL: GLYCEROL
sequence DH
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_D_1506


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