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5NDW

Crystal structure of aminoglycoside TC007 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, E
(1, 5)
25S ribosomal RNApolymer33961097493.92REF (831416132)Saccharomyces cerevisiae S288c
2B, F
(2, 6)
18S ribosomal RNApolymer1800579761.92REF (831416132)Saccharomyces cerevisiae S288c
3C, G
(3, 7)
5S ribosomal RNApolymer12138951.12GenBank (1039024062)Saccharomyces cerevisiae
4D, H
(4, 8)
5.8S ribosomal RNApolymer15850682.92GenBank (1102645687)Saccharomyces cerevisiae
5I, J
(C0, c0)
40S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6K, L
(C1, c1)
40S ribosomal protein S11-Apolymer15617785.92UniProt (P0CX47)
Pfam (PF00366)
Pfam (PF16205)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
7M, N
(C2, c2)
40S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
8O, P
(C3, c3)
40S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
9Q, R
(C4, c4)
40S ribosomal protein S14-Bpolymer12813560.52UniProt (P39516)
Pfam (PF00411)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59B
10S, T
(C5, c5)
40S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RIG protein,RP52,S21,YS21
11U, V
(C6, c6)
40S ribosomal protein S16-Apolymer14115659.22UniProt (P0CX51)
Pfam (PF00380)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
12W, X
(C7, c7)
40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP51A
13Y, Z
(C8, c8)
40S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
14AA, BA
(C9, c9)
40S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,YP45,YS16A
15CA, DA
(d0, D0)
40S ribosomal protein S20polymer10712190.22UniProt (P38701)
Pfam (PF00338)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16EA, FA
(d1, D1)
40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S26,YS25
17GA, HA
(d2, D2)
40S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
18IA, JA
(d3, D3)
40S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
19KA, LA
(d4, D4)
40S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
20MA, NA
(d5, D5)
40S ribosomal protein S25-Apolymer708001.42UniProt (Q3E792)
Pfam (PF03297)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP45,S31,YS23
21OA, PA
(d6, D6)
40S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
22QA, RA
(d7, D7)
40S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
23SA, TA
(d8, D8)
40S ribosomal protein S28-Apolymer637116.32UniProt (Q3E7X9)
Pfam (PF01200)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
24UA, VA
(d9, D9)
40S ribosomal protein S29-Apolymer536335.32UniProt (P41057)
Pfam (PF00253)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S36,YS29
25WA, XA
(e0, E0)
40S ribosomal protein S30-Apolymer616878.22UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
26YA, ZA
(e1, E1)
Ubiquitin-40S ribosomal protein S31polymer738388.02UniProt (P05759)
Pfam (PF01599)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
27AB, BB
(l2, L2)
60S ribosomal protein L2-Apolymer25227217.32UniProt (P0CX45)
Pfam (PF03947)
Pfam (PF00181)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
28CB, DB
(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
29EB, FB
(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
30GB, HB
(l5, L5)
60S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF14204)
Pfam (PF17144)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
31IB, JB
(l6, L6)
60S ribosomal protein L6-Apolymer17620000.62UniProt (Q02326)
Pfam (PF01159)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
32KB, LB
(l7, L7)
60S ribosomal protein L7-Apolymer22325341.52UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
33MB, NB
(l8, L8)
60S ribosomal protein L8-Apolymer23325815.02UniProt (P17076)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
34OB, PB
(l9, L9)
60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
35QB, RB
(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
36SB, TB
(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
37UB, VB
(m3, M3)
60S ribosomal protein L13-Apolymer19421956.32UniProt (Q12690)
Pfam (PF01294)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
38WB, XB
(m4, M4)
60S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
39YB, ZB
(m5, M5)
60S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
40AC, BC
(m6, M6)
60S ribosomal protein L16-Apolymer19722029.02UniProt (P26784)
Pfam (PF00572)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
41CC, DC
(m7, M7)
60S ribosomal protein L17-Apolymer18420589.52UniProt (P05740)
Pfam (PF00237)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
42EC, FC
(m8, M8)
60S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
43GC, HC
(m9, M9)
60S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
44IC, JC
(n0, N0)
60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
45KC, LC
(n1, N1)
60S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
46MC, NC
(n2, N2)
60S ribosomal protein L22-Apolymer10011263.92UniProt (P05749)
Pfam (PF01776)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
47OC, PC
(n3, N3)
60S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
48QC, RC
(n4, N4)
60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
49SC, TC
(n5, N5)
60S ribosomal protein L25polymer12113771.22UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
50UC, VC
(n6, N6)
60S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
51WC, XC
(n7, N7)
60S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
52YC, ZC
(n8, N8)
60S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
53AD, BD
(n9, N9)
60S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
54CD, DD
(o0, O0)
60S ribosomal protein L30polymer10010902.72UniProt (P14120)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
55ED, FD
(o1, O1)
60S ribosomal protein L31-Apolymer10912649.82UniProt (P0C2H8)
Pfam (PF01198)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
56GD, HD
(o2, O2)
60S ribosomal protein L32polymer12714478.12UniProt (P38061)
Pfam (PF01655)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
57ID, JD
(o3, O3)
60S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
58KD, LD
(o4, O4)
60S ribosomal protein L34-Apolymer11212608.82UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
59MD, ND
(o5, O5)
60S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
60OD, PD
(o6, O6)
60S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
61QD, RD
(o7, O7)
60S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
62SD, TD
(o8, O8)
60S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
63UD, VD
(o9, O9)
60S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
64WD, XD
(q0, Q0)
Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
65YD, ZD
(q1, Q1)
60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
Saccharomyces cerevisiae (Baker's yeast)L47,YL41
66AE, BE
(q2, Q2)
60S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
67CE, DE
(q3, Q3)
60S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
68EE, FE
(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
69GE, HE
(S1, s1)
40S ribosomal protein S1-Apolymer21624498.42UniProt (P33442)
Pfam (PF01015)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP10A
70IE, JE
(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
71KE, LE
(S3, s3)
40S ribosomal protein S3polymer22324702.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP13,YS3
72ME, NE
(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
73OE, PE
(S5, s5)
40S ribosomal protein S5polymer20622908.32UniProt (P26783)
Pfam (PF00177)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
74QE, RE
(S6, s6)
40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
75SE, TE
(s7, S7)
40S ribosomal protein S7-Apolymer18421000.52UniProt (P26786)
Pfam (PF01251)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
76UE, VE
(s8, S8)
40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
77WE, XE
(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
78YE, 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
79AF, BF
(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
80AAA, AAB, ABA, ABB, ACA...
(2, 6, c1, 4, L2...)
MAGNESIUM IONnon-polymer24.31365Chemie (MG)
81AWA, AY, BDA, BY, CDA...
(5, 1, 2, 6, 4...)
TC007non-polymer483.525Chemie (8UZ)
82AGB, CGB, GGB, JGB, MGB...
(o4, O4, o7, O7, q0...)
ZINC IONnon-polymer65.417Chemie (ZN)
83AIB, AJB, BIB, BJB, CIB...
(D6, N6, d9, n8, l2...)
waterwater18.01705Chemie (HOH)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains158
Total formula weight6141730.8
Non-Polymers*Number of molecules1407
Total formula weight46376.1
All*Total formula weight6188106.9
*Water molecules are not included.

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PDB entries from 2025-07-09

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