5NDW
Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome
This is a non-PDB format compatible entry.
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | 1, 5 | 25S ribosomal RNA | polymer | 3396 | 1097493.9 | 2 | REF (831416132) | Saccharomyces cerevisiae S288c | |
2 | 2, 6 | 18S ribosomal RNA | polymer | 1800 | 579761.9 | 2 | REF (831416132) | Saccharomyces cerevisiae S288c | |
3 | 3, 7 | 5S ribosomal RNA | polymer | 121 | 38951.1 | 2 | GenBank (1039024062) | Saccharomyces cerevisiae | |
4 | 4, 8 | 5.8S ribosomal RNA | polymer | 158 | 50682.9 | 2 | GenBank (1102645687) | Saccharomyces cerevisiae | |
5 | C0, c0 | 40S ribosomal protein S10-A | polymer | 105 | 12757.4 | 2 | UniProt (Q08745) Pfam (PF03501) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
6 | C1, c1 | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 2 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP41,S18,YS12 |
7 | C2, c2 | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 2 | UniProt (P48589) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
8 | C3, c3 | 40S ribosomal protein S13 | polymer | 150 | 16928.7 | 2 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S27a,YS15 |
9 | C4, c4 | 40S ribosomal protein S14-B | polymer | 128 | 13560.5 | 2 | UniProt (P39516) Pfam (PF00411) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP59B |
10 | C5, c5 | 40S ribosomal protein S15 | polymer | 141 | 15900.7 | 2 | UniProt (Q01855) Pfam (PF00203) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RIG protein,RP52,S21,YS21 |
11 | C6, c6 | 40S ribosomal protein S16-A | polymer | 141 | 15659.2 | 2 | UniProt (P0CX51) Pfam (PF00380) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61R |
12 | C7, c7 | 40S ribosomal protein S17-A | polymer | 136 | 15820.4 | 2 | UniProt (P02407) Pfam (PF00833) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP51A |
13 | C8, c8 | 40S ribosomal protein S18-A | polymer | 145 | 16940.4 | 2 | UniProt (P0CX55) Pfam (PF00416) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
14 | C9, c9 | 40S ribosomal protein S19-A | polymer | 143 | 15810.9 | 2 | UniProt (P07280) Pfam (PF01090) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP55A,S16a,YP45,YS16A |
15 | d0, D0 | 40S ribosomal protein S20 | polymer | 107 | 12190.2 | 2 | UniProt (P38701) Pfam (PF00338) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
16 | d1, D1 | 40S ribosomal protein S21-A | polymer | 87 | 9758.8 | 2 | UniProt (P0C0V8) Pfam (PF01249) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S26,YS25 |
17 | d2, D2 | 40S ribosomal protein S22-A | polymer | 129 | 14518.9 | 2 | UniProt (P0C0W1) Pfam (PF00410) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50,S24,YP58,YS22 |
18 | d3, D3 | 40S ribosomal protein S23-A | polymer | 144 | 15942.7 | 2 | UniProt (P0CX29) Pfam (PF00164) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP37,S28,YS14 |
19 | d4, D4 | 40S ribosomal protein S24-A | polymer | 134 | 15231.6 | 2 | UniProt (P0CX31) Pfam (PF01282) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50 |
20 | d5, D5 | 40S ribosomal protein S25-A | polymer | 70 | 8001.4 | 2 | UniProt (Q3E792) Pfam (PF03297) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP45,S31,YS23 |
21 | d6, D6 | 40S ribosomal protein S26-B | polymer | 97 | 11023.0 | 2 | UniProt (P39939) Pfam (PF01283) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
22 | d7, D7 | 40S ribosomal protein S27-A | polymer | 81 | 8762.2 | 2 | UniProt (P35997) Pfam (PF01667) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61,YS20 |
23 | d8, D8 | 40S ribosomal protein S28-A | polymer | 63 | 7116.3 | 2 | UniProt (Q3E7X9) Pfam (PF01200) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S33,YS27 |
24 | d9, D9 | 40S ribosomal protein S29-A | polymer | 53 | 6335.3 | 2 | UniProt (P41057) Pfam (PF00253) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S36,YS29 |
25 | e0, E0 | 40S ribosomal protein S30-A | polymer | 61 | 6878.2 | 2 | UniProt (P0CX33) Pfam (PF04758) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
26 | e1, E1 | Ubiquitin-40S ribosomal protein S31 | polymer | 73 | 8388.0 | 2 | UniProt (P05759) Pfam (PF01599) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
27 | l2, L2 | 60S ribosomal protein L2-A | polymer | 252 | 27217.3 | 2 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L5,RP8,YL6 |
28 | l3, L3 | 60S ribosomal protein L3 | polymer | 386 | 43719.6 | 2 | UniProt (P14126) Pfam (PF00297) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
29 | l4, L4 | 60S ribosomal protein L4-A | polymer | 361 | 39027.9 | 2 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L2,RP2,YL2 |
30 | l5, L5 | 60S ribosomal protein L5 | polymer | 296 | 33633.6 | 2 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L1,L1a,Ribosomal 5S RNA-binding protein,YL3 |
31 | l6, L6 | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 2 | UniProt (Q02326) Pfam (PF01159) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L17,RP18,YL16 |
32 | l7, L7 | 60S ribosomal protein L7-A | polymer | 223 | 25341.5 | 2 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L6,RP11,YL8 |
33 | l8, L8 | 60S ribosomal protein L8-A | polymer | 233 | 25815.0 | 2 | UniProt (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 |
34 | l9, L9 | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 2 | UniProt (P05738) Pfam (PF00347) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L8,RP24,YL11 |
35 | m0, M0 | 60S ribosomal protein L10 | polymer | 221 | 25410.5 | 2 | UniProt (P41805) Pfam (PF00252) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
36 | m1, M1 | 60S ribosomal protein L11-B | polymer | 169 | 19266.1 | 2 | UniProt (Q3E757) Pfam (PF00281) Pfam (PF00673) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L16,RP39,YL22 |
37 | m3, M3 | 60S ribosomal protein L13-A | polymer | 194 | 21956.3 | 2 | UniProt (Q12690) Pfam (PF01294) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
38 | m4, M4 | 60S ribosomal protein L14-A | polymer | 137 | 15063.9 | 2 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
39 | m5, M5 | 60S ribosomal protein L15-A | polymer | 203 | 24351.2 | 2 | UniProt (P05748) Pfam (PF00827) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L13,RP15R,YL10,YP18 |
40 | m6, M6 | 60S ribosomal protein L16-A | polymer | 197 | 22029.0 | 2 | UniProt (P26784) Pfam (PF00572) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L13a,L21,RP22,YL15 |
41 | m7, M7 | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 2 | UniProt (P05740) Pfam (PF00237) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L20A,YL17 |
42 | m8, M8 | 60S ribosomal protein L18-A | polymer | 185 | 20478.1 | 2 | UniProt (P0CX49) Pfam (PF17135) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP28 |
43 | m9, M9 | 60S ribosomal protein L19-A | polymer | 188 | 21631.1 | 2 | UniProt (P0CX82) Pfam (PF01280) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L23,RP15L,RP33,YL14 |
44 | n0, N0 | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 2 | UniProt (P0CX23) Pfam (PF01775) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L18a |
45 | n1, N1 | 60S ribosomal protein L21-A | polymer | 159 | 18148.1 | 2 | UniProt (Q02753) Pfam (PF01157) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
46 | n2, N2 | 60S ribosomal protein L22-A | polymer | 100 | 11263.9 | 2 | UniProt (P05749) Pfam (PF01776) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L1c,RP4,YL31 |
47 | n3, N3 | 60S ribosomal protein L23-A | polymer | 136 | 14362.8 | 2 | UniProt (P0CX41) Pfam (PF00238) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L17a,YL32 |
48 | n4, N4 | 60S ribosomal protein L24-A | polymer | 155 | 17661.7 | 2 | UniProt (P04449) Pfam (PF01246) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L30,RP29,YL21 |
49 | n5, N5 | 60S ribosomal protein L25 | polymer | 121 | 13771.2 | 2 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP16L,YL25,YP42' |
50 | n6, N6 | 60S ribosomal protein L26-A | polymer | 126 | 14134.6 | 2 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L33,YL33 |
51 | n7, N7 | 60S ribosomal protein L27-A | polymer | 135 | 15437.2 | 2 | UniProt (P0C2H6) Pfam (PF01777) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
52 | n8, N8 | 60S ribosomal protein L28 | polymer | 148 | 16630.5 | 2 | UniProt (P02406) Pfam (PF00828) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L27a,L29,RP44,RP62,YL24 |
53 | n9, N9 | 60S ribosomal protein L29 | polymer | 58 | 6560.7 | 2 | UniProt (P05747) Pfam (PF01779) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | YL43 |
54 | o0, O0 | 60S ribosomal protein L30 | polymer | 100 | 10902.7 | 2 | UniProt (P14120) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L32,RP73,YL38 |
55 | o1, O1 | 60S ribosomal protein L31-A | polymer | 109 | 12649.8 | 2 | UniProt (P0C2H8) Pfam (PF01198) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L34,YL28 |
56 | o2, O2 | 60S ribosomal protein L32 | polymer | 127 | 14478.1 | 2 | UniProt (P38061) Pfam (PF01655) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
57 | o3, O3 | 60S ribosomal protein L33-A | polymer | 106 | 12045.9 | 2 | UniProt (P05744) Pfam (PF01247) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L37,RP47,YL37 |
58 | o4, O4 | 60S ribosomal protein L34-A | polymer | 112 | 12608.8 | 2 | UniProt (P87262) Pfam (PF01199) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
59 | o5, O5 | 60S ribosomal protein L35-A | polymer | 119 | 13811.4 | 2 | UniProt (P0CX84) Pfam (PF00831) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
60 | o6, O6 | 60S ribosomal protein L36-A | polymer | 99 | 11020.1 | 2 | UniProt (P05745) Pfam (PF01158) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L39,YL39 |
61 | o7, O7 | 60S ribosomal protein L37-A | polymer | 87 | 9746.2 | 2 | UniProt (P49166) Pfam (PF01907) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L43,YL35,YP55 |
62 | o8, O8 | 60S ribosomal protein L38 | polymer | 77 | 8714.4 | 2 | UniProt (P49167) Pfam (PF01781) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
63 | o9, O9 | 60S ribosomal protein L39 | polymer | 50 | 6227.4 | 2 | UniProt (P04650) Pfam (PF00832) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L46,YL40 |
64 | q0, Q0 | Ubiquitin-60S ribosomal protein L40 | polymer | 52 | 6032.3 | 2 | UniProt (P0CH08) Pfam (PF01020) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
65 | q1, Q1 | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 2 | UniProt (P0CX86) Pfam (PF05162) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L47,YL41 |
66 | q2, Q2 | 60S ribosomal protein L42-A | polymer | 105 | 12115.5 | 2 | UniProt (P0CX27) Pfam (PF00935) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L41,YL27,YP44 |
67 | q3, Q3 | 60S ribosomal protein L43-A | polymer | 91 | 9981.8 | 2 | UniProt (P0CX25) Pfam (PF01780) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L37a,YL35 |
68 | S0, s0 | 40S ribosomal protein S0-A | polymer | 206 | 22811.1 | 2 | UniProt (P32905) Pfam (PF00318) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nucleic acid-binding protein NAB1A |
69 | S1, s1 | 40S ribosomal protein S1-A | polymer | 216 | 24498.4 | 2 | UniProt (P33442) Pfam (PF01015) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP10A |
70 | S2, s2 | 40S ribosomal protein S2 | polymer | 217 | 23213.0 | 2 | UniProt (P25443) Pfam (PF00333) Pfam (PF03719) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Omnipotent suppressor protein SUP44,RP12,S4,YS5 |
71 | S3, s3 | 40S ribosomal protein S3 | polymer | 223 | 24702.8 | 2 | UniProt (P05750) Pfam (PF07650) Pfam (PF00189) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP13,YS3 |
72 | S4, s4 | 40S ribosomal protein S4-A | polymer | 260 | 29338.1 | 2 | UniProt (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 |
73 | S5, s5 | 40S ribosomal protein S5 | polymer | 206 | 22908.3 | 2 | UniProt (P26783) Pfam (PF00177) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP14,S2,YS8 |
74 | S6, s6 | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 2 | UniProt (P0CX37) Pfam (PF01092) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP9,S10,YS4 |
75 | s7, S7 | 40S ribosomal protein S7-A | polymer | 184 | 21000.5 | 2 | UniProt (P26786) Pfam (PF01251) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP30,RP40 |
76 | s8, S8 | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 2 | UniProt (P0CX39) Pfam (PF01201) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP19,S14,YS9 |
77 | S9, s9 | 40S ribosomal protein S9-A | polymer | 185 | 21210.7 | 2 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP21,S13,YP28,YS11 |
78 | sM, SM | Suppressor protein STM1 | polymer | 272 | 29916.8 | 2 | UniProt (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 |
79 | sR, SR | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 318 | 34710.0 | 2 | UniProt (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 |
80 | 2, 6, c1, 4, L2... | MAGNESIUM ION | non-polymer | 24.3 | 1365 | Chemie (MG) | |||
81 | 5, 1, 2, 6, 4... | TC007 | non-polymer | 483.5 | 25 | Chemie (8UZ) | |||
82 | o4, O4, o7, O7, q0... | ZINC ION | non-polymer | 65.4 | 17 | Chemie (ZN) | |||
83 | water | water | 18.0 | 1705 | Chemie (HOH) |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 158 |
Total formula weight | 6141730.8 | |
Non-Polymers* | Number of molecules | 1407 |
Total formula weight | 46376.1 | |
All* | Total formula weight | 6188106.9 |