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

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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 B:  KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILP
LRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLA
KARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGY
VYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLED
AIEADQTFEMLMGDVVENRRQFIEDNAVYINERNITSEMR
ESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMT
PDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSY
RYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDI
NKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGM
ATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFP
TAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRI
VVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLR
TGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALV
NGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAH
ILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSE
KQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETIL
ADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG
Description (1)  DNA gyrase subunit B, DNA gyrase subunit A/DNA Complex


Functional site

1) chain B
residue 508
type
ligand
sequence D
description binding site for residue MN B 1501
source : AC1

2) chain B
residue 510
type
ligand
sequence D
description binding site for residue MN B 1501
source : AC1

3) chain B
residue 630
type
ligand
sequence R
description binding site for residue 94K B 1502
source : AC2

4) chain B
residue 633
type
ligand
sequence I
description binding site for residue 94K B 1502
source : AC2

5) chain B
residue 634
type
ligand
sequence E
description binding site for residue 94K B 1502
source : AC2

6) chain B
residue 1031
type
ligand
sequence V
description binding site for residue 94K B 1502
source : AC2

7) chain B
residue 1179
type
ligand
sequence M
description binding site for residue 94K B 1502
source : AC2

8) chain B
residue 1342
type
ligand
sequence R
description binding site for residue 94K B 1502
source : AC2

9) chain B
residue 1343
type
ligand
sequence P
description binding site for residue 94K B 1502
source : AC2

10) chain B
residue 1251
type
ligand
sequence E
description binding site for residue GOL B 1503
source : AC3

11) chain B
residue 1255
type
ligand
sequence G
description binding site for residue GOL B 1503
source : AC3

12) chain B
residue 1256
type
ligand
sequence R
description binding site for residue GOL B 1503
source : AC3

13) chain B
residue 1047
type
ligand
sequence R
description binding site for residue GOL B 1504
source : AC4

14) chain B
residue 1048
type
ligand
sequence R
description binding site for residue GOL B 1504
source : AC4

15) chain B
residue 1147
type
ligand
sequence I
description binding site for residue GOL B 1504
source : AC4

16) chain B
residue 1156
type
ligand
sequence E
description binding site for residue GOL B 1504
source : AC4

17) chain B
residue 1190
type
ligand
sequence E
description binding site for residue GOL B 1505
source : AC5

18) chain B
residue 1214
type
ligand
sequence E
description binding site for residue GOL B 1505
source : AC5

19) chain B
residue 1482
type
ligand
sequence D
description binding site for residue GOL B 1505
source : AC5

20) chain B
residue 1483
type
ligand
sequence D
description binding site for residue GOL B 1505
source : AC5

21) chain B
residue 1484
type
ligand
sequence R
description binding site for residue GOL B 1505
source : AC5

22) chain B
residue 1322
type
ligand
sequence Y
description binding site for residue NA B 1506
source : AC6

23) chain B
residue 1323
type
ligand
sequence K
description binding site for residue NA B 1506
source : AC6

24) chain B
residue 1325
type
ligand
sequence T
description binding site for residue NA B 1506
source : AC6

25) chain B
residue 1328
type
ligand
sequence Q
description binding site for residue NA B 1506
source : AC6

26) chain B
residue 1097
type
ligand
sequence F
description binding site for residue DMS B 1507
source : AC7

27) chain B
residue 1113
type
ligand
sequence M
description binding site for residue DMS B 1507
source : AC7

28) chain B
residue 1115
type
ligand
sequence G
description binding site for residue DMS B 1507
source : AC7

29) chain B
residue 1244
type
ligand
sequence R
description binding site for residue GOL D 1504
source : AD2

30) chain B
residue 1319
type
ligand
sequence N
description binding site for residue GOL D 1504
source : AD2

31) chain B
residue 1084
type
ligand
sequence S
description binding site for residue GOL A 101
source : AD5

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

33) chain B
residue 1072
type
ligand
sequence G
description binding site for residue 6EJ C 101
source : AD6

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

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

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

37) chain B
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_B_1502

38) chain B
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_B_1502

39) chain B
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_B_1502

40) chain B
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_B_1502

41) chain B
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_B_1502

42) chain B
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_B_1502

43) chain B
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_B_1502

44) chain B
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_B_1502

45) chain B
residue 1032
type binding
ligand GOL: GLYCEROL
sequence A
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1504

46) chain B
residue 1044
type binding
ligand GOL: GLYCEROL
sequence P
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1504

47) chain B
residue 1047-1048
type binding
ligand GOL: GLYCEROL
sequence RR
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1504

48) chain B
residue 1147
type binding
ligand GOL: GLYCEROL
sequence I
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1504

49) chain B
residue 1156-1158
type binding
ligand GOL: GLYCEROL
sequence EPS
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1504

50) chain B
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

51) chain B
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

52) chain B
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

53) chain B
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

54) chain B
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

55) chain B
residue 1084-1085
type binding
ligand GOL: GLYCEROL
sequence SS
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_A_101

56) chain B
residue 1097
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence F
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_5npp_B_1507

57) chain B
residue 1112-1115
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence SMDG
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_5npp_B_1507

58) chain B
residue 1267-1269
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence QVN
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_5npp_B_1507

59) chain B
residue 1187
type binding
ligand GOL: GLYCEROL
sequence N
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1505

60) chain B
residue 1189-1190
type binding
ligand GOL: GLYCEROL
sequence TE
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1505

61) chain B
residue 1214
type binding
ligand GOL: GLYCEROL
sequence E
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1505

62) chain B
residue 1482-1484
type binding
ligand GOL: GLYCEROL
sequence DDR
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1505

63) chain B
residue 1251-1253
type binding
ligand GOL: GLYCEROL
sequence ERG
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1503

64) chain B
residue 1255-1257
type binding
ligand GOL: GLYCEROL
sequence GRQ
description GLYCEROL binding site
source pdb_hetatom : GOL_5npp_B_1503


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