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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

4U4O

Crystal structure of Geneticin 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 (1262303)Saccharomyces cerevisiae ATCC 204508 / S288cRNA (1750-MER)
2B, CC
(S0, s0)		40S ribosomal protein S0-Apolymer25127920.12UniProt (P32905)
Pfam (PF00318)		Saccharomyces cerevisiae ATCC 204508 / S288cNucleic acid-binding protein NAB1A
3C, DC
(S1, s1)		40S ribosomal protein S1-Apolymer25428667.32UniProt (P33442)
Pfam (PF01015)		Saccharomyces cerevisiae ATCC 204508 / S288cRP10A
4D, EC
(S2, s2)		40S ribosomal protein S2polymer25327359.62UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)		Saccharomyces cerevisiae ATCC 204508 / S288cOmnipotent suppressor protein SUP44,RP12,S4,YS5
5E, FC
(S3, s3)		40S ribosomal protein S3polymer23926411.62UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)		Saccharomyces cerevisiae ATCC 204508 / S288cRP13,YS3
6F, GC
(S4, s4)		40S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)		Saccharomyces cerevisiae ATCC 204508 / S288cRP5,S7,YS6
7G, HC
(S5, s5)		40S ribosomal protein S5polymer22424941.42UniProt (P26783)
Pfam (PF00177)		Saccharomyces cerevisiae ATCC 204508 / S288cRP14,S2,YS8
8H, IC
(S6, s6)		40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)		Saccharomyces cerevisiae ATCC 204508 / S288cRP9,S10,YS4
9I, JC
(S7, s7)		40S ribosomal protein S7-Apolymer18921527.02UniProt (P26786)
Pfam (PF01251)		Saccharomyces cerevisiae ATCC 204508 / S288cRP30,RP40
10J, KC
(S8, s8)		40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)		Saccharomyces cerevisiae ATCC 204508 / S288cRP19,S14,YS9
11K, LC
(S9, s9)		40S ribosomal protein S9-Apolymer19622356.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)		Saccharomyces cerevisiae ATCC 204508 / S288cRP21,S13,YP28,YS11
12L, MC
(C0, c0)		40S ribosomal protein S10-Apolymer10512771.52UniProt (Q08745)
Pfam (PF03501)		Saccharomyces cerevisiae ATCC 204508 / S288c
13M, NC
(C1, c1)		40S ribosomal protein S11-Apolymer15517668.82UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)		Saccharomyces cerevisiae ATCC 204508 / S288cRP41,S18,YS12
14N, OC
(C2, c2)		40S ribosomal protein S12polymer14215385.52UniProt (P48589)
Pfam (PF01248)		Saccharomyces cerevisiae ATCC 204508 / S288c
15O, PC
(C3, c3)		40S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)		Saccharomyces cerevisiae ATCC 204508 / S288cS27a,YS15
16P, QC
(C4, c4)		40S ribosomal protein S14-Apolymer13614431.52UniProt (P06367)
Pfam (PF00411)		Saccharomyces cerevisiae ATCC 204508 / S288cRP59A
17Q, RC
(C5, c5)		40S ribosomal protein S15polymer14115830.62UniProt (Q01855)
Pfam (PF00203)		Saccharomyces cerevisiae ATCC 204508 / S288cRIG protein,RP52,S21,YS21
18R, SC
(C6, c6)		40S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)		Saccharomyces cerevisiae ATCC 204508 / S288cRP61R
19S, TC
(C7, c7)		40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)		Saccharomyces cerevisiae ATCC 204508 / S288cRP51A
20T, UC
(C8, c8)		40S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)		Saccharomyces cerevisiae ATCC 204508 / S288c
21U, VC
(C9, c9)		40S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)		Saccharomyces cerevisiae ATCC 204508 / S288cRP55A,S16a,YP45,YS16A
22V, WC
(D0, d0)		40S ribosomal protein S20polymer12013797.92UniProt (P38701)
Pfam (PF00338)		Saccharomyces cerevisiae ATCC 204508 / S288c
23W, XC
(D1, d1)		40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)		Saccharomyces cerevisiae ATCC 204508 / S288cS26,YS25
24X, YC
(D2, d2)		40S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)		Saccharomyces cerevisiae ATCC 204508 / S288cRP50,S24,YP58,YS22
25Y, ZC
(D3, d3)		40S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)		Saccharomyces cerevisiae ATCC 204508 / S288cRP37,S28,YS14
26AD, Z
(D4, d4)		40S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)		Saccharomyces cerevisiae ATCC 204508 / S288cRP50
27AA, BD
(D5, d5)		40S ribosomal protein S25-Apolymer10711936.12UniProt (Q3E792)
Pfam (PF03297)		Saccharomyces cerevisiae ATCC 204508 / S288cRP45,S31,YS23
28BA, CD
(D6, d6)		40S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)		Saccharomyces cerevisiae ATCC 204508 / S288c
29CA, DD
(D7, d7)		40S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)		Saccharomyces cerevisiae ATCC 204508 / S288cRP61,YS20
30DA, ED
(D8, d8)		40S ribosomal protein S28-Apolymer667474.72UniProt (Q3E7X9)
Pfam (PF01200)		Saccharomyces cerevisiae ATCC 204508 / S288cS33,YS27
31EA, FD
(D9, d9)		40S ribosomal protein S29-Apolymer556544.52UniProt (P41057)
Pfam (PF00253)		Saccharomyces cerevisiae ATCC 204508 / S288cS36,YS29
32FA
(E0)		40S ribosomal protein S30-Apolymer606779.11UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae ATCC 204508 / S288c
33GA
(E1)		Ubiquitin-40S ribosomal protein S31polymer768717.51UniProt (P05759)
Pfam (PF01599)		Saccharomyces cerevisiae ATCC 204508 / S288c
34HA, ID
(SR, sR)		Guanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)		Saccharomyces cerevisiae ATCC 204508 / S288cReceptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35IA, JD
(SM, sM)		Suppressor protein STM1polymer27330048.02UniProt (P39015)
Pfam (PF09598)		Saccharomyces cerevisiae ATCC 204508 / S288c3BP1,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 RNApolymer33961097493.92Saccharomyces cerevisiae ATCC 204508 / S288cRNA (3149-MER)
37KA, LD
(3, 7)		5S ribosomal RNApolymer12138951.12Saccharomyces cerevisiae ATCC 204508 / S288cRNA (121-MER)
38LA, MD
(4, 8)		5.8S ribosomal RNApolymer15850682.92GenBank (618731124)Saccharomyces cerevisiae ATCC 204508 / S288c
39MA, ND
(L2, l2)		60S ribosomal protein L2-Apolymer25327332.42UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae ATCC 204508 / S288cL5,RP8,YL6
40NA, OD
(L3, l3)		60S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae ATCC 204508 / S288cMaintenance 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 ATCC 204508 / S288cL2,RP2,YL2
42PA, QD
(L5, l5)		60S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae ATCC 204508 / S288cL1,L1a,Ribosomal 5S RNA-binding protein,YL3
43QA, RD
(L6, l6)		60S ribosomal protein L6-Apolymer17519869.42UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae ATCC 204508 / S288cL17,RP18,YL16
44RA, SD
(L7, l7)		60S ribosomal protein L7-Apolymer24327555.12UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)		Saccharomyces cerevisiae ATCC 204508 / S288cL6,RP11,YL8
45SA, TD
(L8, l8)		60S ribosomal protein L8-Apolymer25528044.62UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae ATCC 204508 / S288cL4,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 ATCC 204508 / S288cL8,RP24,YL11
47UA, VD
(M0, m0)		60S ribosomal protein L10polymer22025279.32UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae ATCC 204508 / S288cL9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48VA, WD
(M1, m1)		60S ribosomal protein L11-Bpolymer17319654.52UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae ATCC 204508 / S288cL16,RP39,YL22
49WA, YD
(M3, m3)		60S ribosomal protein L13-Apolymer19822473.02UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae ATCC 204508 / S288c
50XA, ZD
(M4, m4)		60S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae ATCC 204508 / S288c
51AE, YA
(M5, m5)		60S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae ATCC 204508 / S288cL13,RP15R,YL10,YP18
52BE, ZA
(M6, m6)		60S ribosomal protein L16-Apolymer19822116.02UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae ATCC 204508 / S288cL13a,L21,RP22,YL15
53AB, CE
(M7, m7)		60S ribosomal protein L17-Apolymer18320458.32UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae ATCC 204508 / S288cL20A,YL17
54BB, DE
(M8, m8)		60S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae ATCC 204508 / S288cRP28
55CB, EE
(M9, m9)		60S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)		Saccharomyces cerevisiae ATCC 204508 / S288cL23,RP15L,RP33,YL14
56DB, FE
(N0, n0)		60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae ATCC 204508 / S288cL18a
57EB, GE
(N1, n1)		60S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae ATCC 204508 / S288c
58FB, HE
(N2, n2)		60S ribosomal protein L22-Apolymer12013580.22UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae ATCC 204508 / S288cL1c,RP4,YL31
59GB, IE
(N3, n3)		60S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae ATCC 204508 / S288cL17a,YL32
60HB, JE
(N4, n4)		60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae ATCC 204508 / S288cL30,RP29,YL21
61IB, KE
(N5, n5)		60S ribosomal protein L25polymer14115656.42UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae ATCC 204508 / S288cRP16L,YL25,YP42'
62JB, LE
(N6, n6)		60S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae ATCC 204508 / S288cL33,YL33
63KB, ME
(N7, n7)		60S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae ATCC 204508 / S288c
64LB, NE
(N8, n8)		60S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae ATCC 204508 / S288cL27a,L29,RP44,RP62,YL24
65MB, OE
(N9, n9)		60S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae ATCC 204508 / S288cYL43
66NB, PE
(O0, o0)		60S ribosomal protein L30polymer10411299.22UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae ATCC 204508 / S288cL32,RP73,YL38
67OB, QE
(O1, o1)		60S ribosomal protein L31-Apolymer11212849.02UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae ATCC 204508 / S288cL34,YL28
68PB, RE
(O2, o2)		60S ribosomal protein L32polymer12914678.22UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae ATCC 204508 / S288c
69QB, SE
(O3, o3)		60S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae ATCC 204508 / S288cL37,RP47,YL37
70RB, TE
(O4, o4)		60S ribosomal protein L34-Apolymer11913412.82UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae ATCC 204508 / S288c
71SB, UE
(O5, o5)		60S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae ATCC 204508 / S288c
72TB, VE
(O6, o6)		60S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae ATCC 204508 / S288cL39,YL39
73UB, WE
(O7, o7)		60S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae ATCC 204508 / S288cL43,YL35,YP55
74VB, XE
(O8, o8)		60S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae ATCC 204508 / S288c
75WB, YE
(O9, o9)		60S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae ATCC 204508 / S288cL46,YL40
76XB, ZE
(Q0, q0)		Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)		Saccharomyces cerevisiae ATCC 204508 / S288c
77AF, YB
(Q1, q1)		60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)		Saccharomyces cerevisiae ATCC 204508 / S288cL47,YL41
78BF, ZB
(Q2, q2)		60S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae ATCC 204508 / S288cL41,YL27,YP44
79AC, CF
(Q3, q3)		60S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae ATCC 204508 / S288cL37a,YL35
80GD
(e0)		40S ribosomal protein S30-Apolymer627006.31UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae ATCC 204508 / S288c
81HD
(e1)		Ubiquitin-40S ribosomal protein S31polymer768703.51UniProt (P05759)
Pfam (PF01599)		Saccharomyces cerevisiae ATCC 204508 / S288c
82XD
(m2)		unknown protein chain m2polymer16013634.81Saccharomyces cerevisiae ATCC 204508 / S288c
83DF
(p0)		60S acidic ribosomal protein P0polymer31133617.91UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)		Saccharomyces cerevisiae ATCC 204508 / S288cA0,L10E
84EF
(p1)		unknown protein chain p1polymer474017.91Saccharomyces cerevisiae ATCC 204508 / S288c
85FF
(p2)		unknown protein chain p2polymer463932.81Saccharomyces cerevisiae ATCC 204508 / S288c
86AAA, AAB, AAC, ABA, ABC...
(1, N0, 5, 6, 2...)		MAGNESIUM IONnon-polymer24.31410Chemie (MG)
87AHB, AHC, AIB, AIC, AJA...
(6, 5, 1, 2, 3...)		osmium (III) hexamminenon-polymer286.41131Chemie (OHX)
88AQ
(2)		GENETICINnon-polymer496.61Chemie (GET)
89ABB, DZC, GZC, LZC, MQ...
(Q3, o7, q0, q2, D6...)		ZINC IONnon-polymer65.416Chemie (ZN)
Sequence modifications
C0, c0: 1 - 105 (UniProt: Q08745)
PDBExternal DatabaseDetails
Ala 89Gly 89conflict
C1, c1: 2 - 156 (UniProt: P0CX47)
PDBExternal DatabaseDetails
Ala 147Gly 147conflict
C2, c2: 2 - 143 (UniProt: P48589)
PDBExternal DatabaseDetails
Ala 104Gly 104conflict
Ala 110Gly 110conflict
C5, c5: 2 - 142 (UniProt: Q01855)
PDBExternal DatabaseDetails
Ser 137Arg 137conflict
O4, o4: 2 - 109 (UniProt: P87262)
PDBExternal DatabaseDetails
Glu 110-expression tag
Ala 111-expression tag
Ala 112-expression tag
Lys 113-expression tag
Ser 114-expression tag
Glu 115-expression tag
Lys 116-expression tag
Lys 117-expression tag
Ala 118-expression tag
Lys 119-expression tag
Lys 120-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains162
Total formula weight6271048.5
Non-Polymers*Number of molecules2558
Total formula weight359692.0
All*Total formula weight6630740.4
*Water molecules are not included.

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PDB entries from 2024-10-30

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