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4GKH

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NA-PP1

Functional Information from GO Data
ChainGOidnamespacecontents
A0005524molecular_functionATP binding
A0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
A0046677biological_processresponse to antibiotic
B0005524molecular_functionATP binding
B0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
B0046677biological_processresponse to antibiotic
C0005524molecular_functionATP binding
C0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
C0046677biological_processresponse to antibiotic
D0005524molecular_functionATP binding
D0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
D0046677biological_processresponse to antibiotic
E0005524molecular_functionATP binding
E0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
E0046677biological_processresponse to antibiotic
F0005524molecular_functionATP binding
F0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
F0046677biological_processresponse to antibiotic
G0005524molecular_functionATP binding
G0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
G0046677biological_processresponse to antibiotic
H0005524molecular_functionATP binding
H0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
H0046677biological_processresponse to antibiotic
I0005524molecular_functionATP binding
I0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
I0046677biological_processresponse to antibiotic
J0005524molecular_functionATP binding
J0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
J0046677biological_processresponse to antibiotic
K0005524molecular_functionATP binding
K0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
K0046677biological_processresponse to antibiotic
L0005524molecular_functionATP binding
L0016773molecular_functionphosphotransferase activity, alcohol group as acceptor
L0046677biological_processresponse to antibiotic
Functional Information from PDB Data
site_idAC1
Number of Residues21
DetailsBINDING SITE FOR RESIDUE KAN A 301
ChainResidue
AGLN35
AGLU269
APHE271
AHOH405
AHOH427
AHOH450
AHOH480
AHOH482
AHOH491
AHOH661
BSER2
AASP165
BHIS3
KARG6
APHE166
AASP167
AASP198
AARG219
AASN234
ACYS235
AASP268

site_idAC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0J9 A 302
ChainResidue
AASP31
AILE40
APHE53
APRO82
ATHR99
AALA100
AILE101
AILE215
AACT305
AHOH409
BGLN5

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 303
ChainResidue
AGLY159
AHOH456
CHOH536
KHOH426
KHOH474
KHOH605

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT A 304
ChainResidue
AVAL109
ASER116
AGLY209
AHOH511

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT A 305
ChainResidue
AVAL33
ATHR105
AASP202
A0J9302
BHOH453

site_idAC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE ACT A 306
ChainResidue
AGLY37
ATHR39
AHIS56
AGLY57
ALYS58
AVAL61
AHOH597

site_idAC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE KAN B 301
ChainResidue
BASP165
BASP167
BASP198
BASN234
BCYS235
BGLU238
BASP268
BGLU269
BPHE271
BHOH404
BHOH432
BHOH433
BHOH434
BHOH539
BHOH540
BHOH552
BHOH559
BHOH573
BHOH597
BHOH640
HGLY252
HASP254

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE 0J9 B 302
ChainResidue
BILE40
BPHE53
BPRO82
BILE101
BASP216

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 303
ChainResidue
BTHR76
BMSE79
BHOH528
BHOH631
BHOH647

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 304
ChainResidue
BASN234
BHOH432
BHOH458
BHOH474
BHOH486

site_idBC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE ACT B 305
ChainResidue
BTYR113
BSER116

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE ACT B 306
ChainResidue
BHOH605
BGLY37
BALA38
BTHR39
BHIS56
BLYS58
BVAL61

site_idBC4
Number of Residues23
DetailsBINDING SITE FOR RESIDUE KAN C 301
ChainResidue
CGLN35
CASP165
CASP167
CASP198
CARG219
CASN234
CCYS235
CGLU238
CASP268
CGLU269
CPHE271
CHOH423
CHOH430
CHOH448
CHOH455
CHOH459
CHOH463
CHOH508
CHOH518
CHOH546
CHOH588
CHOH620
CHOH636

site_idBC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 0J9 C 302
ChainResidue
CASP31
CASN32
CPHE53
CPRO82
CALA100
CILE101
CILE215
CHOH425
CHOH462
DGLN5

site_idBC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE 0J9 C 303
ChainResidue
CGLN5
DPHE53
DPRO82
DTHR99
DILE101
DASP216
DHOH475

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA C 304
ChainResidue
CTHR76
CMSE79
CACT307
CHOH449
CHOH533

site_idBC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL C 305
ChainResidue
CGLN35
CSER36
CALA38

site_idBC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT C 306
ChainResidue
CVAL109
CSER116
CGLY209

site_idCC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT C 307
ChainResidue
CTHR76
CALA77
CMSE79
CPRO80
CNA304

site_idCC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT C 308
ChainResidue
CARG30
HLEU243
HHOH498

site_idCC3
Number of Residues19
DetailsBINDING SITE FOR RESIDUE KAN D 301
ChainResidue
DASP165
DASP167
DASP198
DASN234
DCYS235
DGLU238
DASP268
DGLU269
DPHE271
DHOH414
DHOH415
DHOH418
DHOH420
DHOH429
DHOH433
DHOH512
DHOH527
DHOH538
DHOH556

site_idCC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT D 302
ChainResidue
DGLY37
DTHR39
DHIS56
DGLY57
DLYS58
DVAL61

site_idCC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT D 303
ChainResidue
DPRO187
DPHE188
DSER189
DHOH453
IARG14

site_idCC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT D 304
ChainResidue
DPHE107
DGLU111
DGLU238
LGLU176

site_idCC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT D 305
ChainResidue
DTHR76
DALA77
DMSE79
DPRO80
DARG130

site_idCC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEG D 306
ChainResidue
DARG129
DSER133
DARG225
DTYR251
DHOH567

site_idCC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PEG D 307
ChainResidue
DTYR113
DASN119
DGLY209

site_idDC1
Number of Residues22
DetailsBINDING SITE FOR RESIDUE KAN E 301
ChainResidue
EGLN35
EASP165
EPHE166
EASP167
EASP198
EARG219
EASN234
EASP268
EGLU269
EPHE271
EHOH403
EHOH407
EHOH420
EHOH425
EHOH427
EHOH462
EHOH496
EHOH512
FSER2
FHIS3
FHOH488
GARG6

site_idDC2
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0J9 E 302
ChainResidue
EASP31
EILE40
EPHE53
EPRO82
EALA100
EILE101
EILE215
EASP216
EACT306
EHOH413
EHOH439
FGLN5

site_idDC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA E 303
ChainResidue
EGLY159
EHOH482
GHOH413
GHOH473
IHOH660

site_idDC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT E 304
ChainResidue
EGLY37
ETHR39
EHIS56
EGLY57
ELYS58
EVAL61

site_idDC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT E 305
ChainResidue
EVAL109
ESER116
EGLY209
EHOH459

site_idDC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT E 306
ChainResidue
EVAL33
EASP202
E0J9302
FGLN5

site_idDC7
Number of Residues21
DetailsBINDING SITE FOR RESIDUE KAN F 301
ChainResidue
FASP165
FASP167
FASP198
FARG219
FASN234
FCYS235
FGLU238
FASP268
FGLU269
FPHE271
FHOH409
FHOH415
FHOH429
FHOH432
FHOH446
FHOH468
FHOH477
FHOH492
FHOH507
FHOH528
LGLY252

site_idDC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE 0J9 F 302
ChainResidue
FASN32
FPHE53
FPRO82
FILE101
FILE215
FHOH506

site_idDC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA F 303
ChainResidue
FTHR76
FMSE79
FHOH486
FHOH623
FHOH643

site_idEC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA F 304
ChainResidue
FASN234
FHOH409
FHOH419
FHOH453
FHOH462

site_idEC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT F 305
ChainResidue
FVAL109
FTYR113
FGLY209

site_idEC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT F 306
ChainResidue
FMSE258
FGLN262
FHOH500

site_idEC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT F 307
ChainResidue
FARG129
FARG225
FTYR251
FHOH565
FHOH625

site_idEC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE ACT F 308
ChainResidue
FGLY37
FALA38
FTHR39
FHIS56
FGLY57
FLYS58
FVAL61
FHOH586

site_idEC6
Number of Residues21
DetailsBINDING SITE FOR RESIDUE KAN G 301
ChainResidue
GASP165
GASP167
GASP198
GASN234
GCYS235
GGLU238
GASP268
GGLU269
GPHE271
GHOH411
GHOH414
GHOH422
GHOH431
GHOH448
GHOH480
GHOH482
GHOH483
GHOH495
GHOH504
GHOH579
IGLY252

site_idEC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE 0J9 G 302
ChainResidue
GPHE53
GPRO82
GILE101
GILE215
GHOH585
GHOH649

site_idEC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA G 303
ChainResidue
GTHR76
GMSE79
GACT306
GHOH539
GHOH575

site_idEC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA G 304
ChainResidue
GASN234
GHOH411
GHOH421
GHOH453
GHOH467

site_idFC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT G 305
ChainResidue
GVAL109
GTYR113
GSER116
GILE120

site_idFC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT G 306
ChainResidue
GALA77
GPHE78
GMSE79
GPRO80
GNA303

site_idFC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT G 307
ChainResidue
GTRP233
GMSE258
GGLN262
GHOH486

site_idFC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE KAN H 301
ChainResidue
GSER2
GHIS3
GHOH503
HASP165
HASP167
HASP198
HASN234
HCYS235
HGLU238
HASP268
HGLU269
HPHE271
HHOH424
HHOH429
HHOH439
HHOH443
HHOH448
HHOH478
HHOH499
HHOH511
HHOH548

site_idFC5
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0J9 H 302
ChainResidue
GGLN5
HASP31
HVAL33
HPHE53
HPRO82
HALA100
HILE101
HILE215
HASP216
HACT304
HHOH407
HHOH467

site_idFC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA H 303
ChainResidue
HTHR76
HMSE79
HACT305
HHOH529
HHOH530

site_idFC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT H 304
ChainResidue
GHOH449
HASP202
H0J9302

site_idFC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT H 305
ChainResidue
HTHR76
HALA77
HPHE78
HMSE79
HPRO80
HNA303

site_idFC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PEG H 306
ChainResidue
DARG14
HSER116

site_idGC1
Number of Residues23
DetailsBINDING SITE FOR RESIDUE KAN I 301
ChainResidue
FARG6
FHOH476
IGLN35
IASP165
IASP167
IASP198
IARG219
IASN234
ICYS235
IGLU238
IASP268
IGLU269
IPHE271
IHOH424
IHOH425
IHOH447
IHOH494
IHOH507
IHOH542
IHOH558
IHOH600
JSER2
JHOH496

site_idGC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 0J9 I 302
ChainResidue
IASP31
IILE40
IPHE53
IPRO82
IALA100
IILE101
IILE215
IASP216
IHOH446
JGLN5

site_idGC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA I 303
ChainResidue
ITHR76
IMSE79
IACT305
IHOH456
IHOH492

site_idGC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL I 304
ChainResidue
IGLN35
ISER36
IALA38
ILYS55
IHOH476

site_idGC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT I 305
ChainResidue
ITHR76
IALA77
IPHE78
IMSE79
IPRO80
INA303

site_idGC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE ACT I 306
ChainResidue
ISER116
IHOH644

site_idGC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT I 307
ChainResidue
IASP202
IHOH653
JGLN5

site_idGC8
Number of Residues17
DetailsBINDING SITE FOR RESIDUE KAN J 301
ChainResidue
AHOH536
JASP165
JASP167
JASP198
JASN234
JCYS235
JASP268
JGLU269
JPHE271
JHOH409
JHOH426
JHOH435
JHOH436
JHOH454
JHOH468
JHOH483
JHOH540

site_idGC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE 0J9 J 302
ChainResidue
JASP31
JILE40
JPHE53
JPRO82
JTHR99
JALA100
JILE101
JHOH516

site_idHC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE ACT J 303
ChainResidue
JGLY37
JALA38
JTHR39
JHIS56
JGLY57
JLYS58
JVAL61

site_idHC2
Number of Residues23
DetailsBINDING SITE FOR RESIDUE KAN K 301
ChainResidue
CGLY252
CASP254
CHOH403
KASP165
KASP167
KASP198
KASN234
KCYS235
KGLU238
KASP268
KGLU269
KPHE271
KHOH409
KHOH421
KHOH429
KHOH462
KHOH463
KHOH505
KHOH506
KHOH513
KHOH528
KHOH529
KHOH584

site_idHC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE 0J9 K 302
ChainResidue
KASP31
KPHE53
KPRO82
KTHR99
KILE101
KHOH559
KHOH582
KHOH598

site_idHC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA K 303
ChainResidue
KTHR76
KMSE79
KHOH481
KHOH601
KHOH658

site_idHC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA K 304
ChainResidue
CHOH403
KASN234
KHOH424
KHOH459
KHOH485

site_idHC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT K 305
ChainResidue
KTRP233
KMSE258
KGLN262
KHOH547

site_idHC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT K 306
ChainResidue
KTYR113
KSER116
KGLY209
KHOH647

site_idHC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT K 307
ChainResidue
KGLY37
KALA38
KHIS56
KGLY57
KLYS58
KVAL61

site_idHC9
Number of Residues21
DetailsBINDING SITE FOR RESIDUE KAN L 301
ChainResidue
JARG6
KSER2
KHIS3
LASP165
LASP167
LASP198
LASN234
LCYS235
LGLU238
LASP268
LGLU269
LPHE271
LHOH422
LHOH439
LHOH442
LHOH463
LHOH465
LHOH469
LHOH490
LHOH521
LHOH652

site_idIC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 0J9 L 302
ChainResidue
LASP31
LVAL33
LPHE53
LPRO82
LALA100
LILE101
LILE215
LASP216
LACT308
LHOH408
LHOH487

site_idIC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA L 303
ChainResidue
LTHR76
LMSE79
LACT305
LHOH527
LHOH530

site_idIC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE ACT L 304
ChainResidue
LASP20
LTYR24

site_idIC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE ACT L 305
ChainResidue
FGLN35
LTHR76
LALA77
LPHE78
LMSE79
LPRO80
LNA303

site_idIC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT L 307
ChainResidue
LMSE258
LLEU261
LGLN262
LHOH631

site_idIC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT L 308
ChainResidue
KGLN5
LTHR105
LASP202
L0J9302
LHOH473

Functional Information from PROSITE/UniProt
site_idPS00109
Number of Residues13
DetailsPROTEIN_KINASE_TYR Tyrosine protein kinases specific active-site signature. VTHgDFSLDNLIF
ChainResidueDetails
AVAL194-PHE206

227111

PDB entries from 2024-11-06

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