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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

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
11, 525S ribosomal RNApolymer33961097493.92REF (831416132)Saccharomyces cerevisiae S288c
22, 618S ribosomal RNApolymer1800579761.92REF (831416132)Saccharomyces cerevisiae S288c
33, 75S ribosomal RNApolymer12138951.12GenBank (1039024062)Saccharomyces cerevisiae
44, 85.8S ribosomal RNApolymer15850682.92GenBank (1102645687)Saccharomyces cerevisiae
5C0, c040S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6C1, c140S ribosomal protein S11-Apolymer15617785.92UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
7C2, c240S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
8C3, c340S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
9C4, c440S ribosomal protein S14-Bpolymer12813560.52UniProt (P39516)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59B
10C5, c540S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RIG protein,RP52,S21,YS21
11C6, c640S ribosomal protein S16-Apolymer14115659.22UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
12C7, c740S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP51A
13C8, c840S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
14C9, c940S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,YP45,YS16A
15d0, D040S ribosomal protein S20polymer10712190.22UniProt (P38701)
Pfam (PF00338)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16d1, D140S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S26,YS25
17d2, D240S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
18d3, D340S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
19d4, D440S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
20d5, D540S ribosomal protein S25-Apolymer708001.42UniProt (Q3E792)
Pfam (PF03297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP45,S31,YS23
21d6, D640S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
22d7, D740S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
23d8, D840S ribosomal protein S28-Apolymer637116.32UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
24d9, D940S ribosomal protein S29-Apolymer536335.32UniProt (P41057)
Pfam (PF00253)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S36,YS29
25e0, E040S ribosomal protein S30-Apolymer616878.22UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
26e1, E1Ubiquitin-40S ribosomal protein S31polymer738388.02UniProt (P05759)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
27l2, L260S ribosomal protein L2-Apolymer25227217.32UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
28l3, L360S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
29l4, L460S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
30l5, L560S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
31l6, L660S ribosomal protein L6-Apolymer17620000.62UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
32l7, L760S ribosomal protein L7-Apolymer22325341.52UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
33l8, L860S ribosomal protein L8-Apolymer23325815.02UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
34l9, L960S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
35m0, M060S ribosomal protein L10polymer22125410.52UniProt (P41805)
Pfam (PF00252)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
36m1, M160S ribosomal protein L11-Bpolymer16919266.12UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
37m3, M360S ribosomal protein L13-Apolymer19421956.32UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
38m4, M460S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
39m5, M560S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
40m6, M660S ribosomal protein L16-Apolymer19722029.02UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
41m7, M760S ribosomal protein L17-Apolymer18420589.52UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
42m8, M860S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
43m9, M960S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
44n0, N060S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
45n1, N160S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
46n2, N260S ribosomal protein L22-Apolymer10011263.92UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
47n3, N360S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
48n4, N460S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
49n5, N560S ribosomal protein L25polymer12113771.22UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
50n6, N660S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
51n7, N760S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
52n8, N860S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
53n9, N960S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
54o0, O060S ribosomal protein L30polymer10010902.72UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
55o1, O160S ribosomal protein L31-Apolymer10912649.82UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
56o2, O260S ribosomal protein L32polymer12714478.12UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
57o3, O360S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
58o4, O460S ribosomal protein L34-Apolymer11212608.82UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
59o5, O560S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
60o6, O660S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
61o7, O760S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
62o8, O860S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
63o9, O960S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
64q0, Q0Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
65q1, Q160S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L47,YL41
66q2, Q260S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
67q3, Q360S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
68S0, s040S ribosomal protein S0-Apolymer20622811.12UniProt (P32905)
Pfam (PF00318)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleic acid-binding protein NAB1A
69S1, s140S ribosomal protein S1-Apolymer21624498.42UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP10A
70S2, s240S ribosomal protein S2polymer21723213.02UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,YS5
71S3, s340S ribosomal protein S3polymer22324702.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP13,YS3
72S4, s440S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP5,S7,YS6
73S5, s540S ribosomal protein S5polymer20622908.32UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
74S6, s640S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
75s7, S740S ribosomal protein S7-Apolymer18421000.52UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
76s8, S840S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
77S9, s940S ribosomal protein S9-Apolymer18521210.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP21,S13,YP28,YS11
78sM, SMSuppressor protein STM1polymer27229916.82UniProt (P39015)
Pfam (PF09598)
In PDB		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
79sR, SRGuanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
802, 6, c1, 4, L2...MAGNESIUM IONnon-polymer24.31365Chemie (MG)
815, 1, 2, 6, 4...TC007non-polymer483.525Chemie (8UZ)
82o4, O4, o7, O7, q0...ZINC IONnon-polymer65.417Chemie (ZN)
83waterwater18.01705Chemie (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 2024-07-17

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