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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)
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 (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
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)
81AAA, AAB, AAC, ABA, ABB...
(1, 5, 7, 8, m0...)
MAGNESIUM IONnon-polymer24.32139Chemie (MG)
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.

246031

PDB entries from 2025-12-10

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