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4OX9

Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit

Functional Information from GO Data
ChainGOidnamespacecontents
B0003735molecular_functionstructural constituent of ribosome
B0005840cellular_componentribosome
B0006412biological_processtranslation
B0015935cellular_componentsmall ribosomal subunit
B0019843molecular_functionrRNA binding
B0022627cellular_componentcytosolic small ribosomal subunit
B1990904cellular_componentribonucleoprotein complex
C0003676molecular_functionnucleic acid binding
C0003723molecular_functionRNA binding
C0003729molecular_functionmRNA binding
C0003735molecular_functionstructural constituent of ribosome
C0005840cellular_componentribosome
C0006412biological_processtranslation
C0019843molecular_functionrRNA binding
C0022627cellular_componentcytosolic small ribosomal subunit
C1990904cellular_componentribonucleoprotein complex
D0003723molecular_functionRNA binding
D0003735molecular_functionstructural constituent of ribosome
D0005840cellular_componentribosome
D0006412biological_processtranslation
D0015935cellular_componentsmall ribosomal subunit
D0019843molecular_functionrRNA binding
D0042274biological_processribosomal small subunit biogenesis
D0046872molecular_functionmetal ion binding
D1990904cellular_componentribonucleoprotein complex
E0003723molecular_functionRNA binding
E0003735molecular_functionstructural constituent of ribosome
E0005737cellular_componentcytoplasm
E0005840cellular_componentribosome
E0006412biological_processtranslation
E0015935cellular_componentsmall ribosomal subunit
E0019843molecular_functionrRNA binding
E0043229cellular_componentintracellular organelle
E1990904cellular_componentribonucleoprotein complex
F0003735molecular_functionstructural constituent of ribosome
F0005737cellular_componentcytoplasm
F0005840cellular_componentribosome
F0006412biological_processtranslation
F0019843molecular_functionrRNA binding
F0022627cellular_componentcytosolic small ribosomal subunit
F0043229cellular_componentintracellular organelle
F0070181molecular_functionsmall ribosomal subunit rRNA binding
F1990904cellular_componentribonucleoprotein complex
G0000028biological_processribosomal small subunit assembly
G0000049molecular_functiontRNA binding
G0003723molecular_functionRNA binding
G0003729molecular_functionmRNA binding
G0003735molecular_functionstructural constituent of ribosome
G0005840cellular_componentribosome
G0006412biological_processtranslation
G0015935cellular_componentsmall ribosomal subunit
G0019843molecular_functionrRNA binding
G0022627cellular_componentcytosolic small ribosomal subunit
G1990904cellular_componentribonucleoprotein complex
H0003735molecular_functionstructural constituent of ribosome
H0005840cellular_componentribosome
H0006412biological_processtranslation
I0000049molecular_functiontRNA binding
I0003723molecular_functionRNA binding
I0003735molecular_functionstructural constituent of ribosome
I0005737cellular_componentcytoplasm
I0005840cellular_componentribosome
I0006412biological_processtranslation
I0019843molecular_functionrRNA binding
I0043232cellular_componentintracellular non-membrane-bounded organelle
I1990904cellular_componentribonucleoprotein complex
J0000049molecular_functiontRNA binding
J0003723molecular_functionRNA binding
J0003735molecular_functionstructural constituent of ribosome
J0005840cellular_componentribosome
J0006412biological_processtranslation
J0015935cellular_componentsmall ribosomal subunit
J0019843molecular_functionrRNA binding
J1990904cellular_componentribonucleoprotein complex
K0003735molecular_functionstructural constituent of ribosome
K0005840cellular_componentribosome
K0006412biological_processtranslation
K0019843molecular_functionrRNA binding
K0022627cellular_componentcytosolic small ribosomal subunit
K1990904cellular_componentribonucleoprotein complex
L0000049molecular_functiontRNA binding
L0003735molecular_functionstructural constituent of ribosome
L0005840cellular_componentribosome
L0006412biological_processtranslation
L0015935cellular_componentsmall ribosomal subunit
L0019843molecular_functionrRNA binding
L1990904cellular_componentribonucleoprotein complex
M0000049molecular_functiontRNA binding
M0003676molecular_functionnucleic acid binding
M0003723molecular_functionRNA binding
M0003735molecular_functionstructural constituent of ribosome
M0005829cellular_componentcytosol
M0005840cellular_componentribosome
M0006412biological_processtranslation
M0015935cellular_componentsmall ribosomal subunit
M0019843molecular_functionrRNA binding
M1990904cellular_componentribonucleoprotein complex
N0003735molecular_functionstructural constituent of ribosome
N0005840cellular_componentribosome
N0006412biological_processtranslation
O0003735molecular_functionstructural constituent of ribosome
O0005737cellular_componentcytoplasm
O0005840cellular_componentribosome
O0006412biological_processtranslation
O0019843molecular_functionrRNA binding
O0022627cellular_componentcytosolic small ribosomal subunit
O0043229cellular_componentintracellular organelle
O1990904cellular_componentribonucleoprotein complex
P0003735molecular_functionstructural constituent of ribosome
P0005737cellular_componentcytoplasm
P0005840cellular_componentribosome
P0006412biological_processtranslation
P0015935cellular_componentsmall ribosomal subunit
P0043229cellular_componentintracellular organelle
P1990904cellular_componentribonucleoprotein complex
Q0003735molecular_functionstructural constituent of ribosome
Q0005840cellular_componentribosome
Q0006412biological_processtranslation
R0003735molecular_functionstructural constituent of ribosome
R0005840cellular_componentribosome
R0006412biological_processtranslation
R0019843molecular_functionrRNA binding
R0070181molecular_functionsmall ribosomal subunit rRNA binding
R1990904cellular_componentribonucleoprotein complex
S0000028biological_processribosomal small subunit assembly
S0003723molecular_functionRNA binding
S0003735molecular_functionstructural constituent of ribosome
S0005737cellular_componentcytoplasm
S0005840cellular_componentribosome
S0006412biological_processtranslation
S0015935cellular_componentsmall ribosomal subunit
S0019843molecular_functionrRNA binding
S0022627cellular_componentcytosolic small ribosomal subunit
S0043229cellular_componentintracellular organelle
S1990904cellular_componentribonucleoprotein complex
T0003723molecular_functionRNA binding
T0003735molecular_functionstructural constituent of ribosome
T0005829cellular_componentcytosol
T0005840cellular_componentribosome
T0006412biological_processtranslation
T0015935cellular_componentsmall ribosomal subunit
T0019843molecular_functionrRNA binding
T0070181molecular_functionsmall ribosomal subunit rRNA binding
T1990904cellular_componentribonucleoprotein complex
V0005840cellular_componentribosome
V0019843molecular_functionrRNA binding
V1990904cellular_componentribonucleoprotein complex
Y0008168molecular_functionmethyltransferase activity
Y0032259biological_processmethylation
Y0046677biological_processresponse to antibiotic
Functional Information from PDB Data
site_idAC1
Number of Residues2
Detailsbinding site for residue MG A 1600
ChainResidue
AG703
AC1452

site_idAC2
Number of Residues3
Detailsbinding site for residue MG A 1601
ChainResidue
AG257
AG258
AG266

site_idAC3
Number of Residues1
Detailsbinding site for residue MG A 1603
ChainResidue
AG577

site_idAC4
Number of Residues2
Detailsbinding site for residue MG A 1606
ChainResidue
AG581
AG758

site_idAC5
Number of Residues3
Detailsbinding site for residue MG A 1607
ChainResidue
AG593
AU646
AG592

site_idAC6
Number of Residues3
Detailsbinding site for residue MG A 1608
ChainResidue
AC58
AA59
AU387

site_idAC7
Number of Residues4
Detailsbinding site for residue MG A 1609
ChainResidue
AG11
AU12
AG21
AG22

site_idAC8
Number of Residues2
Detailsbinding site for residue MG A 1610
ChainResidue
AA665
AG666

site_idAC9
Number of Residues1
Detailsbinding site for residue MG A 1611
ChainResidue
AG115

site_idAD1
Number of Residues2
Detailsbinding site for residue MG A 1613
ChainResidue
AU14
AU17

site_idAD2
Number of Residues2
Detailsbinding site for residue MG A 1614
ChainResidue
AG297
AG299

site_idAD3
Number of Residues2
Detailsbinding site for residue MG A 1615
ChainResidue
AG575
AG576

site_idAD4
Number of Residues2
Detailsbinding site for residue MG A 1616
ChainResidue
AA583
AG584

site_idAD5
Number of Residues1
Detailsbinding site for residue MG A 1617
ChainResidue
AG1432

site_idAD6
Number of Residues2
Detailsbinding site for residue MG A 1619
ChainResidue
AG1517
YARG37

site_idAD7
Number of Residues1
Detailsbinding site for residue MG A 1620
ChainResidue
AG377

site_idAD8
Number of Residues1
Detailsbinding site for residue MG A 1621
ChainResidue
AG438

site_idAD9
Number of Residues2
Detailsbinding site for residue MG A 1622
ChainResidue
AC749
AG750

site_idAE1
Number of Residues2
Detailsbinding site for residue MG A 1624
ChainResidue
AA766
AC812

site_idAE2
Number of Residues1
Detailsbinding site for residue MG A 1625
ChainResidue
AA768

site_idAE3
Number of Residues1
Detailsbinding site for residue MG A 1627
ChainResidue
AG774

site_idAE4
Number of Residues1
Detailsbinding site for residue MG A 1628
ChainResidue
AA777

site_idAE5
Number of Residues2
Detailsbinding site for residue MG A 1629
ChainResidue
AG576
AC578

site_idAE6
Number of Residues1
Detailsbinding site for residue MG A 1631
ChainResidue
AG362

site_idAE7
Number of Residues2
Detailsbinding site for residue MG A 1632
ChainResidue
AA453
AC454

site_idAE8
Number of Residues2
Detailsbinding site for residue MG A 1633
ChainResidue
AA509
AA510

site_idAE9
Number of Residues1
Detailsbinding site for residue MG A 1634
ChainResidue
AU560

site_idAF1
Number of Residues1
Detailsbinding site for residue MG A 1636
ChainResidue
AA572

site_idAF2
Number of Residues1
Detailsbinding site for residue MG A 1637
ChainResidue
AG21

site_idAF3
Number of Residues3
Detailsbinding site for residue MG A 1638
ChainResidue
AC48
AU114
AG115

site_idAF4
Number of Residues4
Detailsbinding site for residue MG A 1639
ChainResidue
AG595
AC596
AG597
AU598

site_idAF5
Number of Residues2
Detailsbinding site for residue MG A 1640
ChainResidue
AG837
AG838

site_idAF6
Number of Residues2
Detailsbinding site for residue MG A 1641
ChainResidue
AG858
AG869

site_idAF7
Number of Residues1
Detailsbinding site for residue MG A 1642
ChainResidue
AG570

site_idAF8
Number of Residues1
Detailsbinding site for residue MG A 1643
ChainResidue
AA860

site_idAF9
Number of Residues2
Detailsbinding site for residue MG A 1644
ChainResidue
AG637
AG638

site_idAG1
Number of Residues3
Detailsbinding site for residue MG A 1645
ChainResidue
AG885
AG886
AU911

site_idAG2
Number of Residues1
Detailsbinding site for residue MG A 1646
ChainResidue
AG1385

site_idAG3
Number of Residues2
Detailsbinding site for residue MG A 1647
ChainResidue
AA937
AA938

site_idAG4
Number of Residues2
Detailsbinding site for residue MG A 1648
ChainResidue
AC934
AU1345

site_idAG5
Number of Residues2
Detailsbinding site for residue MG A 1651
ChainResidue
AG1370
AG1371

site_idAG6
Number of Residues3
Detailsbinding site for residue MG A 1655
ChainResidue
AA602
AG635
AU636

site_idAG7
Number of Residues1
Detailsbinding site for residue MG A 1657
ChainResidue
AG588

site_idAG8
Number of Residues2
Detailsbinding site for residue MG A 1659
ChainResidue
AG944
AG945

site_idAG9
Number of Residues2
Detailsbinding site for residue MG A 1660
ChainResidue
AA964
AU1199

site_idAH1
Number of Residues6
Detailsbinding site for residue MG A 1661
ChainResidue
AC979
AC980
AU981
AU982
AG1221
AG1222

site_idAH2
Number of Residues3
Detailsbinding site for residue MG A 1663
ChainResidue
AG1053
AC1054
AG1197

site_idAH3
Number of Residues4
Detailsbinding site for residue MG A 1664
ChainResidue
AC1054
AU1196
AG1197
AG1198

site_idAH4
Number of Residues3
Detailsbinding site for residue MG A 1665
ChainResidue
TTHR35
AG1441
AG1455

site_idAH5
Number of Residues1
Detailsbinding site for residue MG A 1667
ChainResidue
AG1469

site_idAH6
Number of Residues1
Detailsbinding site for residue MG A 1668
ChainResidue
AA915

site_idAH7
Number of Residues1
Detailsbinding site for residue MG A 1669
ChainResidue
AG301

site_idAH8
Number of Residues4
Detailsbinding site for residue MG A 1670
ChainResidue
AG299
AG558
AU560
AG566

site_idAH9
Number of Residues1
Detailsbinding site for residue MG A 1671
ChainResidue
AG324

site_idAI1
Number of Residues4
Detailsbinding site for residue MG A 1672
ChainResidue
AU516
AG517
AA532
AA533

site_idAI2
Number of Residues3
Detailsbinding site for residue MG A 1673
ChainResidue
AA572
AA573
AA574

site_idAI3
Number of Residues2
Detailsbinding site for residue MG A 1674
ChainResidue
AG649
AG650

site_idAI4
Number of Residues2
Detailsbinding site for residue MG A 1675
ChainResidue
AG595
AU641

site_idAI5
Number of Residues2
Detailsbinding site for residue MG A 1676
ChainResidue
AA608
AG610

site_idAI6
Number of Residues1
Detailsbinding site for residue MG A 1677
ChainResidue
AG888

site_idAI7
Number of Residues1
Detailsbinding site for residue MG A 1678
ChainResidue
AG895

site_idAI8
Number of Residues2
Detailsbinding site for residue MG A 1679
ChainResidue
AA53
AA353

site_idAI9
Number of Residues2
Detailsbinding site for residue MG A 1680
ChainResidue
AA1110
AC1189

site_idAJ1
Number of Residues4
Detailsbinding site for residue MG A 1681
ChainResidue
AA1067
AG1068
AG1094
AG1387

site_idAJ2
Number of Residues2
Detailsbinding site for residue MG A 1682
ChainResidue
AU1095
AG1108

site_idAJ3
Number of Residues1
Detailsbinding site for residue MG A 1683
ChainResidue
AU1083

site_idAJ4
Number of Residues1
Detailsbinding site for residue MG A 1685
ChainResidue
AG1224

site_idAJ5
Number of Residues1
Detailsbinding site for residue MG A 1686
ChainResidue
AG1266

site_idAJ6
Number of Residues5
Detailsbinding site for residue MG A 1689
ChainResidue
AC924
AG925
AU1390
AU1391
AG1392

site_idAJ7
Number of Residues4
Detailsbinding site for residue MG A 1691
ChainResidue
AA1499
AA1500
AG1504
AG1505

site_idAJ8
Number of Residues2
Detailsbinding site for residue MG A 1692
ChainResidue
AG64
AA101

site_idAJ9
Number of Residues2
Detailsbinding site for residue MG A 1695
ChainResidue
AA8
AA298

site_idAK1
Number of Residues2
Detailsbinding site for residue MG A 1696
ChainResidue
AA535
AC536

site_idAK2
Number of Residues2
Detailsbinding site for residue MG A 1697
ChainResidue
AG148
AA172

site_idAK3
Number of Residues1
Detailsbinding site for residue MG A 1698
ChainResidue
AG168

site_idAK4
Number of Residues1
Detailsbinding site for residue MG A 1699
ChainResidue
AA195

site_idAK5
Number of Residues3
Detailsbinding site for residue MG A 1701
ChainResidue
AA116
AG117
AG289

site_idAK6
Number of Residues3
Detailsbinding site for residue MG A 1702
ChainResidue
AG293
AU304
AG305

site_idAK7
Number of Residues2
Detailsbinding site for residue MG A 1703
ChainResidue
AC330
AC352

site_idAK8
Number of Residues4
Detailsbinding site for residue MG A 1704
ChainResidue
AC372
AU375
AG376
AU387

site_idAK9
Number of Residues2
Detailsbinding site for residue MG A 1705
ChainResidue
AG410
AA431

site_idAL1
Number of Residues2
Detailsbinding site for residue MG A 1706
ChainResidue
AC504
AG505

site_idAL2
Number of Residues1
Detailsbinding site for residue MG A 1707
ChainResidue
AG111

site_idAL3
Number of Residues2
Detailsbinding site for residue MG A 1710
ChainResidue
AA782
AA794

site_idAL4
Number of Residues2
Detailsbinding site for residue MG A 1712
ChainResidue
AU133
AU229

site_idAL5
Number of Residues5
Detailsbinding site for residue MG A 1713
ChainResidue
AG1057
AG1058
AC1059
AG1198
AU1199

site_idAL6
Number of Residues2
Detailsbinding site for residue MG A 1715
ChainResidue
AC1303
AG1304

site_idAL7
Number of Residues1
Detailsbinding site for residue MG A 1716
ChainResidue
AG1520

site_idAL8
Number of Residues3
Detailsbinding site for residue MG B 301
ChainResidue
BASP166
BASP191
BASP205

site_idAL9
Number of Residues5
Detailsbinding site for residue ZN D 301
ChainResidue
DCYS9
DCYS12
DLEU19
DCYS26
DCYS31

site_idAM1
Number of Residues2
Detailsbinding site for residue MG E 201
ChainResidue
AU863
EGLU83

site_idAM2
Number of Residues4
Detailsbinding site for residue ZN N 101
ChainResidue
NCYS24
NCYS27
NCYS40
NCYS43

site_idAM3
Number of Residues2
Detailsbinding site for residue MG N 102
ChainResidue
AC980
NALA20

site_idAM4
Number of Residues16
Detailsbinding site for residue SFG Y 301
ChainResidue
AA1408
AC1484
AU1485
YGLY32
YTHR33
YGLY34
YASP55
YPRO56
YALA87
YGLU88
YLEU104
YPHE105
YTHR109
YLEU110
YLEU196
YTRP197

Functional Information from PROSITE/UniProt
site_idPS00052
Number of Residues27
DetailsRIBOSOMAL_S7 Ribosomal protein S7 signature. DvLvtaFInkimrdGKKnlaarIFydA
ChainResidueDetails
GASP20-ALA46

site_idPS00053
Number of Residues18
DetailsRIBOSOMAL_S8 Ribosomal protein S8 signature. GiaILSTSkGVLtdreAR
ChainResidueDetails
HGLY108-ARG125

site_idPS00054
Number of Residues23
DetailsRIBOSOMAL_S11 Ribosomal protein S11 signature. IrALqaS.GLqVksivDdTPvPHN
ChainResidueDetails
KILE95-ASN117

site_idPS00055
Number of Residues8
DetailsRIBOSOMAL_S12 Ribosomal protein S12 signature. KkPNSAlR
ChainResidueDetails
LLYS46-ARG53

site_idPS00056
Number of Residues13
DetailsRIBOSOMAL_S17 Ribosomal protein S17 signature. GDvVeIiEsRPIS
ChainResidueDetails
QGLY54-SER66

site_idPS00057
Number of Residues24
DetailsRIBOSOMAL_S18 Ribosomal protein S18 signature. RDYrn.VevLkrFLSEt.GKIlprRR
ChainResidueDetails
RARG32-ARG55

site_idPS00063
Number of Residues16
DetailsALDOKETO_REDUCTASE_3 Aldo/keto reductase family putative active site signature. LAKTIKraRIlGLlPF
ChainResidueDetails
RLEU66-PHE81

site_idPS00323
Number of Residues25
DetailsRIBOSOMAL_S19 Ribosomal protein S19 signature. NGKqhvpvyItenmVGhkLGEFapT
ChainResidueDetails
SASN53-THR77

site_idPS00360
Number of Residues19
DetailsRIBOSOMAL_S9 Ribosomal protein S9 signature. GGGksGQidAiklGiARAL
ChainResidueDetails
IGLY67-LEU85

site_idPS00361
Number of Residues16
DetailsRIBOSOMAL_S10 Ribosomal protein S10 signature. ArrsGAqvsGPIpLPT
ChainResidueDetails
JALA27-THR42

site_idPS00362
Number of Residues31
DetailsRIBOSOMAL_S15 Ribosomal protein S15 signature. LseHLkvhKkDhhShrgLlmMvgqrrrLlrY
ChainResidueDetails
OLEU39-TYR69

site_idPS00527
Number of Residues23
DetailsRIBOSOMAL_S14 Ribosomal protein S14 signature. R.CvrcgrarsvyrfFGLCRiCLR
ChainResidueDetails
NARG23-ARG45

site_idPS00548
Number of Residues35
DetailsRIBOSOMAL_S3 Ribosomal protein S3 signature. ARtewaaqGrVplHt..LranIDygfalarTtyGvlG
ChainResidueDetails
CALA163-GLY197

site_idPS00585
Number of Residues33
DetailsRIBOSOMAL_S5 Ribosomal protein S5 signature. GRrfrFgAlvVVGDrq.GrVGlGfgkap.EVpl.AV
ChainResidueDetails
EGLY23-VAL55

site_idPS00632
Number of Residues25
DetailsRIBOSOMAL_S4 Ribosomal protein S4 signature. LEsRLdnvVYRlgfAvSrrqARqLV
ChainResidueDetails
DLEU97-VAL121

site_idPS00646
Number of Residues14
DetailsRIBOSOMAL_S13_1 Ribosomal protein S13 signature. RGlRHrrGlpVRGQ
ChainResidueDetails
MARG88-GLN101

site_idPS00962
Number of Residues12
DetailsRIBOSOMAL_S2_1 Ribosomal protein S2 signature 1. VkELLEAGVHFG
ChainResidueDetails
BVAL7-GLY18

site_idPS01048
Number of Residues10
DetailsRIBOSOMAL_S6 Ribosomal protein S6 signature. GlRRLAYpIA
ChainResidueDetails
FGLY44-ALA53

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:11866529
ChainResidueDetails
NCYS24
NCYS27
NCYS40
NCYS43

site_idSWS_FT_FI2
Number of Residues3
DetailsBINDING:
ChainResidueDetails
YALA87
YLEU104
YSER195

221716

PDB entries from 2024-06-26

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