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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5NDV

Crystal structure of Paromomycin 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, AC
(1, 5)		25S ribosomal RNApolymer33961097493.92GenBank (834774822)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
2B, BC
(3, 7)		5S ribosomal RNApolymer12138951.12GenBank (1039024062)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
3C, CC
(4, 8)		5.8S ribosomal RNApolymer15850682.92GenBank (1102645687)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
4D, DC
(L2, l2)		60S ribosomal protein L2-Apolymer24826730.72UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
5E, EC
(L3, l3)		60S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
6F, FC
(L4, l4)		60S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
7G, GC
(L5, l5)		60S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
8H, HC
(L6, l6)		60S ribosomal protein L6-Apolymer17620000.62UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
9I, IC
(L7, l7)		60S ribosomal protein L7-Apolymer22625726.92UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
10J, JC
(L8, l8)		60S ribosomal protein L8-Apolymer23125656.82UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
11K, KC
(L9, l9)		60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
12L, LC
(M0, m0)		60S ribosomal protein L10polymer22125410.52UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
13M, MC
(M1, m1)		60S ribosomal protein L11-Bpolymer16919266.12UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
14N, NC
(M3, m3)		60S ribosomal protein L13-Apolymer19421956.32UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15O, OC
(M4, m4)		60S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16P, PC
(M5, m5)		60S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
17Q, QC
(M6, m6)		60S ribosomal protein L16-Apolymer19722029.02UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
18R, RC
(M7, m7)		60S ribosomal protein L17-Apolymer18420589.52UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
19S, SC
(M8, m8)		60S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
20T, TC
(M9, m9)		60S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
Pfam (PF25476)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
21U, UC
(N0, n0)		60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
22V, VC
(N1, n1)		60S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23W, WC
(N2, n2)		60S ribosomal protein L22-Apolymer9911135.72UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
24X, XC
(N3, n3)		60S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
25Y, YC
(N4, n4)		60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
26Z, ZC
(N5, n5)		60S ribosomal protein L25polymer12013642.02UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
27AA, AD
(N6, n6)		60S ribosomal protein L26-Apolymer12514005.52UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
28BA, BD
(N7, n7)		60S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29CA, CD
(N8, n8)		60S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
30DA, DD
(N9, n9)		60S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
31EA, ED
(O0, o0)		60S ribosomal protein L30polymer10010902.72UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
32FA, FD
(O1, o1)		60S ribosomal protein L31-Apolymer11212849.02UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
33GA, GD
(O2, o2)		60S ribosomal protein L32polymer12714478.12UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34HA, HD
(O3, o3)		60S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
35IA, ID
(O4, o4)		60S ribosomal protein L34-Apolymer11212608.82UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
36JA, JD
(O5, o5)		60S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37KA, KD
(O6, o6)		60S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
38LA, LD
(O7, o7)		60S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
39MA, MD
(O8, o8)		60S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
40NA, ND
(O9, o9)		60S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
41OA, OD
(Q0, q0)		Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
42PA, PD
(Q1, q1)		60S ribosomal protein L41-Bpolymer253354.22UniProt (P0CX87)
Pfam (PF05162)		Saccharomyces cerevisiae (Baker's yeast)L47,YL41
43QA, QD
(Q2, q2)		60S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
44RA, RD
(Q3, q3)		60S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
45SA, SD
(2, 6)		18S ribosomal RNApolymer1800579761.92GenBank (874346701)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
46TA, TD
(S0, s0)		40S ribosomal protein S0-Apolymer20622811.12UniProt (P32905)
Pfam (PF00318)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleic acid-binding protein NAB1A
47UA, UD
(S1, s1)		40S ribosomal protein S1-Apolymer21624498.42UniProt (B3RHV0)
Pfam (PF01015)
UniProt (by SIFTS) (P33442)		Saccharomyces cerevisiae (strain RM11-1a) (Baker's yeast)
48VA, VD
(S2, s2)		40S ribosomal protein S2polymer21723213.02UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,YS5
49WA, WD
(S3, s3)		40S ribosomal protein S3polymer22324702.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP13,YS3
50XA, XD
(S4, s4)		40S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Pfam (PF08071)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP5,S7,YS6
51YA, YD
(S5, s5)		40S ribosomal protein S5polymer20622908.32UniProt (P26783)
Pfam (PF00177)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
52ZA
(S6)		40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
53AB, AE
(S7, s7)		40S ribosomal protein S7-Apolymer18621158.62UniProt (P26786)
Pfam (PF01251)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
54BB, BE
(S8, s8)		40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
55CB, CE
(S9, s9)		40S ribosomal protein S9-Apolymer18521210.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP21,S13,YP28,YS11
56DB, DE
(C0, c0)		40S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
57EB, EE
(C1, c1)		40S ribosomal protein S11-Apolymer14616588.52UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
58FB, FE
(C2, c2)		40S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
59GB, GE
(C3, c3)		40S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
60HB, HE
(C4, c4)		40S ribosomal protein S14-Bpolymer12813560.52UniProt (P39516)
Pfam (PF00411)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59B
61IB, IE
(C5, c5)		40S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RIG protein,RP52,S21,YS21
62JB, JE
(C6, c6)		40S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
63KB, KE
(C7, c7)		40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP51A
64LB, LE
(C8, c8)		40S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
65MB, ME
(C9, c9)		40S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,YP45,YS16A
66NB, NE
(D0, d0)		40S ribosomal protein S20polymer10912447.42UniProt (P38701)
Pfam (PF00338)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
67OB, OE
(D1, d1)		40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S26,YS25
68PB, PE
(D2, d2)		40S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
69QB, QE
(D3, d3)		40S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
70RB, RE
(D4, d4)		40S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
71SB, SE
(D5, d5)		40S ribosomal protein S25-Apolymer708001.42UniProt (Q3E792)
Pfam (PF03297)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP45,S31,YS23
72TB, TE
(D6, d6)		40S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
73UB, UE
(D7, d7)		40S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
74VB, VE
(D8, d8)		40S ribosomal protein S28-Apolymer637116.32UniProt (Q3E7X9)
Pfam (PF01200)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
75WB, WE
(D9, d9)		40S ribosomal protein S29-Apolymer536335.32UniProt (P41057)
Pfam (PF00253)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S36,YS29
76XB, XE
(E0, e0)		40S ribosomal protein S30-Apolymer627006.32UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
77YB, YE
(SR, sR)		Guanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
78ZB, ZE
(SM, sM)		Suppressor protein STM1polymer27229916.82UniProt (P39015)
Pfam (PF09598)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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
79ZD
(s6)		40S ribosomal protein S6-Apolymer21824966.01UniProt (P0CX37)
Pfam (PF01092)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
80AF, AG, AZA, BF, BFC...
(1, 5, o2, 8, n3...)		PAROMOMYCINnon-polymer615.687Chemie (PAR)
PubChem (16757804)
PubChem (16760604)
PubChem (17757254)
PubChem (20849281)
PubChem (71191297)
PubChem (23789070)
PubChem (24096964)
PubChem (24867526)
PubChem (24867858)
PubChem (25104843)
PubChem (44120093)
PubChem (44251565)
PubChem (71188564)
PubChem (53486370)
PubChem (165580)
PubChem (44186758)
PubChem (58160567)
PubChem (44663324)
PubChem (59361026)
PubChem (59800245)
PubChem (45358711)
PubChem (70793652)
PubChem (70793824)
PubChem (70795918)
PubChem (71068776)
PubChem (71072581)
PubChem (71072592)
PubChem (50989619)
PubChem (66932615)
PubChem (68032118)
PubChem (4689)
PubChem (14951)
PubChem (24176)
PubChem (70878598)
PubChem (71751432)
PubChem (73707499)
PubChem (3040200)
PubChem (91151908)
PubChem (91867972)
PubChem (91972181)
PubChem (94469268)
PubChem (98048759)
PubChem (98048761)
PubChem (5702262)
PubChem (121292209)
PubChem (6603975)
PubChem (6604293)
PubChem (122537356)
PubChem (6710686)
PubChem (124226135)
PubChem (124464537)
PubChem (9809147)
PubChem (125040357)
PubChem (125040359)
PubChem (125121197)
PubChem (94469269)
PubChem (94469270)
PubChem (94469271)
PubChem (129009945)
PubChem (131841783)
PubChem (132275078)
PubChem (6602492)
PubChem (6713982)
PubChem (98048758)
PubChem (98048760)
PubChem (101739930)
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PubChem (118705495)
PubChem (9961808)
PubChem (122691713)
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PubChem (124226132)
PubChem (124226133)
PubChem (124226134)
PubChem (124464538)
PubChem (124761786)
PubChem (124761787)
PubChem (124761788)
PubChem (124761789)
PubChem (152952600)
PubChem (125040358)
PubChem (125040360)
PubChem (125121198)
PubChem (162873319)
PubChem (129014632)
PubChem (129014634)
PubChem (129014635)
PubChem (129313238)
PubChem (134771120)
PubChem (137404838)
PubChem (161153506)
PubChem (163199098)
PubChem (164850471)
PubChem (172091638)
PubChem (173719997)
81AAA, AAB, AAC, ABA, ABB...
(1, 5, 7, 8, m0...)		MAGNESIUM IONnon-polymer24.32139Chemie (MG)
PubChem (888)
82CNC, ENC, EPA, FNC, GFC...
(d6, d7, O7, d9, o4...)		ZINC IONnon-polymer65.416Chemie (ZN)
83AOC, APC, BOC, BPC, COC...
(O3, n3, O4, n6, O7...)		waterwater18.01346Chemie (HOH)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains156
Total formula weight6120839.5
Non-Polymers*Number of molecules2242
Total formula weight106594.6
All*Total formula weight6227434.1
*Water molecules are not included.

253091

PDB entries from 2026-05-06

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