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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5NDG

Crystal structure of geneticin (G418) bound to the yeast 80S ribosome

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, BC
(2, 6)		18S ribosomal RNApolymer1800579761.92GenBank (874346701)Saccharomyces cerevisiae (Baker's yeast)
2B, CC
(S0, s0)		40S ribosomal protein S0-Apolymer20622811.12UniProt (P32905)
Pfam (PF00318)		Saccharomyces cerevisiae (Baker's yeast)Nucleic acid-binding protein NAB1A
3C, DC
(S1, s1)		40S ribosomal protein S1-Apolymer21624498.42UniProt (P33442)
Pfam (PF01015)		Saccharomyces cerevisiae (Baker's yeast)RP10A
4D, EC
(S2, s2)		40S ribosomal protein S2polymer21723213.02UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)		Saccharomyces cerevisiae (Baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,YS5
5E, FC
(S3, s3)		40S ribosomal protein S3polymer22324702.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)		Saccharomyces cerevisiae (Baker's yeast)RP13,YS3
6F, GC
(S4, s4)		40S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)		Saccharomyces cerevisiae (Baker's yeast)RP5,S7,YS6
7G, HC
(S5, s5)		40S ribosomal protein S5polymer20622908.32UniProt (P26783)
Pfam (PF00177)		Saccharomyces cerevisiae (Baker's yeast)RP14,S2,YS8
8H, IC
(S6, s6)		40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)		Saccharomyces cerevisiae (Baker's yeast)RP9,S10,YS4
9I, JC
(S7, s7)		40S ribosomal protein S7-Apolymer18521071.62UniProt (P26786)
Pfam (PF01251)		Saccharomyces cerevisiae (Baker's yeast)RP30,RP40
10J, KC
(S8, s8)		40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)		Saccharomyces cerevisiae (Baker's yeast)RP19,S14,YS9
11K, LC
(S9, s9)		40S ribosomal protein S9-Apolymer18521210.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)		Saccharomyces cerevisiae (Baker's yeast)RP21,S13,YP28,YS11
12L, MC
(C0, c0)		40S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)		Saccharomyces cerevisiae (Baker's yeast)
13M, NC
(C1, c1)		40S ribosomal protein S11-Apolymer15617785.92UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)		Saccharomyces cerevisiae (Baker's yeast)RP41,S18,YS12
14N, OC
(C2, c2)		40S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)		Saccharomyces cerevisiae (Baker's yeast)
15O, PC
(C3, c3)		40S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)		Saccharomyces cerevisiae (Baker's yeast)S27a,YS15
16P, QC
(C4, c4)		40S ribosomal protein S14-Apolymer12813560.52UniProt (P06367)
Pfam (PF00411)		Saccharomyces cerevisiae (Baker's yeast)RP59A
17Q, RC
(C5, c5)		40S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)		Saccharomyces cerevisiae (Baker's yeast)RIG protein,RP52,S21,YS21
18R, SC
(C6, c6)		40S ribosomal protein S16-Apolymer14115659.22UniProt (P0CX51)
Pfam (PF00380)		Saccharomyces cerevisiae (Baker's yeast)RP61R
19S, TC
(C7, c7)		40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)		Saccharomyces cerevisiae (Baker's yeast)RP51A
20T, UC
(C8, c8)		40S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)		Saccharomyces cerevisiae (Baker's yeast)
21U, VC
(C9, c9)		40S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)		Saccharomyces cerevisiae (Baker's yeast)RP55A,S16a,YP45,YS16A
22V, WC
(D0, d0)		40S ribosomal protein S20polymer10712190.22UniProt (P38701)
Pfam (PF00338)		Saccharomyces cerevisiae (Baker's yeast)
23W, XC
(D1, d1)		40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)		Saccharomyces cerevisiae (Baker's yeast)S26,YS25
24X, YC
(D2, d2)		40S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)		Saccharomyces cerevisiae (Baker's yeast)RP50,S24,YP58,YS22
25Y, ZC
(D3, d3)		40S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)		Saccharomyces cerevisiae (Baker's yeast)RP37,S28,YS14
26AD, Z
(D4, d4)		40S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)		Saccharomyces cerevisiae (Baker's yeast)RP50
27AA, BD
(D5, d5)		40S ribosomal protein S25-Apolymer708001.42UniProt (Q3E792)
Pfam (PF03297)		Saccharomyces cerevisiae (Baker's yeast)RP45,S31,YS23
28BA, CD
(D6, d6)		40S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)		Saccharomyces cerevisiae (Baker's yeast)
29CA, DD
(D7, d7)		40S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)		Saccharomyces cerevisiae (Baker's yeast)RP61,YS20
30DA, ED
(D8, d8)		40S ribosomal protein S28-Apolymer637116.32UniProt (Q3E7X9)
Pfam (PF01200)		Saccharomyces cerevisiae (Baker's yeast)S33,YS27
31EA, FD
(D9, d9)		40S ribosomal protein S29-Apolymer536335.32UniProt (P41057)
Pfam (PF00253)		Saccharomyces cerevisiae (Baker's yeast)S36,YS29
32FA, GD
(E0, e0)		40S ribosomal protein S30-Apolymer606779.12UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae (Baker's yeast)
33GA, HD
(E1, e1)		Ubiquitin-40S ribosomal protein S31polymer15217254.22UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)		Saccharomyces cerevisiae (Baker's yeast)
34HA, ID
(SR, sR)		Guanine nucleotide-binding protein subunit beta-like proteinpolymer31834651.92UniProt (P38011)
Pfam (PF00400)		Saccharomyces cerevisiae (Baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35IA, JD
(SM, sM)		Suppressor protein STM1polymer27229916.82UniProt (P39015)
Pfam (PF09598)		Saccharomyces cerevisiae (Baker's yeast)3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
36JA, KD
(1, 5)		25S ribosomal RNApolymer33961097493.92GenBank (834774822)Saccharomyces cerevisiae (Baker's yeast)
37KA, LD
(3, 7)		5S ribosomal RNApolymer12138951.12GenBank (1039024062)Saccharomyces cerevisiae (Baker's yeast)
38LA, MD
(4, 8)		5.8S ribosomal RNApolymer15850682.92GenBank (1102645687)Saccharomyces cerevisiae (Baker's yeast)
39MA, ND
(L2, l2)		60S ribosomal protein L2-Apolymer25227217.32UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae (Baker's yeast)L5,RP8,YL6
40NA, OD
(L3, l3)		60S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
41OA, PD
(L4, l4)		60S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae (Baker's yeast)L2,RP2,YL2
42PA, QD
(L5, l5)		60S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
43QA, RD
(L6, l6)		60S ribosomal protein L6-Apolymer17620000.62UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae (Baker's yeast)L17,RP18,YL16
44RA, SD
(L7, l7)		60S ribosomal protein L7-Apolymer22325341.52UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)		Saccharomyces cerevisiae (Baker's yeast)L6,RP11,YL8
45SA, TD
(L8, l8)		60S ribosomal protein L8-Apolymer23325815.02UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
46TA, UD
(L9, l9)		60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae (Baker's yeast)L8,RP24,YL11
47UA, VD
(M0, m0)		60S ribosomal protein L10polymer22125410.52UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48VA, WD
(M1, m1)		60S ribosomal protein L11-Apolymer16919266.12UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae (Baker's yeast)L16,RP39,YL22
49WA, XD
(M3, m3)		60S ribosomal protein L13-Apolymer19421956.32UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae (Baker's yeast)
50XA, YD
(M4, m4)		60S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae (Baker's yeast)
51YA, ZD
(M5, m5)		60S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae (Baker's yeast)L13,RP15R,YL10,YP18
52AE, ZA
(M6, m6)		60S ribosomal protein L16-Apolymer19722029.02UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae (Baker's yeast)L13a,L21,RP22,YL15
53AB, BE
(M7, m7)		60S ribosomal protein L17-Apolymer18420589.52UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae (Baker's yeast)L20A,YL17
54BB, CE
(M8, m8)		60S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae (Baker's yeast)RP28
55CB, DE
(M9, m9)		60S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
Pfam (PF25476)		Saccharomyces cerevisiae (Baker's yeast)L23,RP15L,RP33,YL14
56DB, EE
(N0, n0)		60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae (Baker's yeast)L18a
57EB, FE
(N1, n1)		60S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae (Baker's yeast)
58FB, GE
(N2, n2)		60S ribosomal protein L22-Apolymer9811006.62UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae (Baker's yeast)L1c,RP4,YL31
59GB, HE
(N3, n3)		60S ribosomal protein L23-Apolymer13514275.72UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae (Baker's yeast)L17a,YL32
60HB, IE
(N4, n4)		60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae (Baker's yeast)L30,RP29,YL21
61IB, JE
(N5, n5)		60S ribosomal protein L25polymer12113771.22UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae (Baker's yeast)RP16L,YL25,YP42'
62JB, KE
(N6, n6)		60S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae (Baker's yeast)L33,YL33
63KB, LE
(N7, n7)		60S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae (Baker's yeast)
64LB, ME
(N8, n8)		60S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae (Baker's yeast)L27a,L29,RP44,RP62,YL24
65MB, NE
(N9, n9)		60S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae (Baker's yeast)YL43
66NB, OE
(O0, o0)		60S ribosomal protein L30polymer10010902.72UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae (Baker's yeast)L32,RP73,YL38
67OB, PE
(O1, o1)		60S ribosomal protein L31-Apolymer10912649.82UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae (Baker's yeast)L34,YL28
68PB, QE
(O2, o2)		60S ribosomal protein L32polymer12714478.12UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae (Baker's yeast)
69QB, RE
(O3, o3)		60S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae (Baker's yeast)L37,RP47,YL37
70RB, SE
(O4, o4)		60S ribosomal protein L34-Apolymer11212608.82UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae (Baker's yeast)
71SB, TE
(O5, o5)		60S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae (Baker's yeast)
72TB, UE
(O6, o6)		60S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae (Baker's yeast)L39,YL39
73UB, VE
(O7, o7)		60S ribosomal protein L37-Apolymer849517.02UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae (Baker's yeast)L43,YL35,YP55
74VB, WE
(O8, o8)		60S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae (Baker's yeast)
75WB, XE
(O9, o9)		60S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae (Baker's yeast)L46,YL40
76XB, YE
(Q0, q0)		Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)		Saccharomyces cerevisiae (Baker's yeast)
77YB, ZE
(Q1, q1)		60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)		Saccharomyces cerevisiae (Baker's yeast)L47,YL41
78AF, ZB
(Q2, q2)		60S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae (Baker's yeast)L41,YL27,YP44
79AC, BF
(Q3, q3)		60S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae (Baker's yeast)L37a,YL35
80CF
(p0)		60S acidic ribosomal protein P0polymer31233749.11UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)		Saccharomyces cerevisiae (Baker's yeast)A0,L10E
81AAA, AAB, ABA, ACA, ADA...
(3, l3, 4, N7, 6...)		MAGNESIUM IONnon-polymer24.31221Chemie (MG)
PubChem (888)
82CHA, DHA, EHA, KJ, LJ...
(6, 2, 5, 1, n6)		GENETICINnon-polymer496.621Chemie (GET)
PubChem (16218859)
PubChem (16401283)
PubChem (16757917)
PubChem (44120012)
PubChem (44658668)
PubChem (46936936)
PubChem (123865)
PubChem (53393459)
PubChem (354578)
PubChem (50990066)
PubChem (71039031)
PubChem (51892360)
PubChem (71308205)
PubChem (447379)
PubChem (71684684)
PubChem (53384376)
PubChem (57383382)
PubChem (2733531)
PubChem (67965674)
PubChem (89798855)
PubChem (89800134)
PubChem (94865123)
PubChem (95065565)
PubChem (95371616)
PubChem (98051603)
PubChem (98484451)
PubChem (117723194)
PubChem (124837660)
PubChem (124837658)
PubChem (125461703)
PubChem (127044571)
PubChem (129014560)
PubChem (129644226)
PubChem (94865112)
PubChem (94865113)
PubChem (94865114)
PubChem (94865115)
PubChem (95371615)
PubChem (95796293)
PubChem (6710770)
PubChem (98046639)
PubChem (98046640)
PubChem (98484453)
PubChem (98484455)
PubChem (98484457)
PubChem (98754175)
PubChem (133640203)
PubChem (118941020)
PubChem (123479690)
PubChem (124081981)
PubChem (124488631)
PubChem (124488632)
PubChem (124504542)
PubChem (142526453)
PubChem (124837659)
PubChem (124837661)
PubChem (124839315)
PubChem (124869842)
PubChem (124869843)
PubChem (124869844)
PubChem (124869845)
PubChem (162888700)
PubChem (168275439)
PubChem (131632479)
PubChem (131664888)
PubChem (134695363)
PubChem (137705473)
PubChem (137967135)
PubChem (140918304)
PubChem (162467978)
PubChem (173972551)
83ABB, CBB, IBB, ICA, JBB...
(o4, o7, q0, O4, q2...)		ZINC IONnon-polymer65.418Chemie (ZN)
84ACB, ADB, BCB, BDB, CCB...
(4, m0, L2, m5, L3...)		waterwater18.01054Chemie (HOH)
Sequence modifications
SR, sR: 2 - 319 (UniProt: P38011)
PDBExternal DatabaseDetails
Ala 161Lys 161conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains159
Total formula weight6191892.7
Non-Polymers*Number of molecules1260
Total formula weight41281.4
All*Total formula weight6233174.1
*Water molecules are not included.

253091

PDB entries from 2026-05-06

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