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 | A, E (1, 5) | 25S ribosomal RNA | polymer | 3396 | 1097493.9 | 2 | REF (831416132) | Saccharomyces cerevisiae S288c | |
2 | B, F (2, 6) | 18S ribosomal RNA | polymer | 1800 | 579761.9 | 2 | REF (831416132) | Saccharomyces cerevisiae S288c | |
3 | C, G (3, 7) | 5S ribosomal RNA | polymer | 121 | 38951.1 | 2 | GenBank (1039024062) | Saccharomyces cerevisiae | |
4 | D, H (4, 8) | 5.8S ribosomal RNA | polymer | 158 | 50682.9 | 2 | GenBank (1102645687) | Saccharomyces cerevisiae | |
5 | I, J (C0, c0) | 40S ribosomal protein S10-A | polymer | 105 | 12757.4 | 2 | UniProt (Q08745) Pfam (PF03501) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
6 | K, L (C1, c1) | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 2 | UniProt (P0CX47) Pfam (PF00366) Pfam (PF16205) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP41,S18,YS12 |
7 | M, N (C2, c2) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 2 | UniProt (P48589) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
8 | O, P (C3, c3) | 40S ribosomal protein S13 | polymer | 150 | 16928.7 | 2 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S27a,YS15 |
9 | Q, R (C4, c4) | 40S ribosomal protein S14-B | polymer | 128 | 13560.5 | 2 | UniProt (P39516) Pfam (PF00411) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP59B |
10 | S, T (C5, c5) | 40S ribosomal protein S15 | polymer | 141 | 15900.7 | 2 | UniProt (Q01855) Pfam (PF00203) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RIG protein,RP52,S21,YS21 |
11 | U, V (C6, c6) | 40S ribosomal protein S16-A | polymer | 141 | 15659.2 | 2 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61R |
12 | W, X (C7, c7) | 40S ribosomal protein S17-A | polymer | 136 | 15820.4 | 2 | UniProt (P02407) Pfam (PF00833) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP51A |
13 | Y, Z (C8, c8) | 40S ribosomal protein S18-A | polymer | 145 | 16940.4 | 2 | UniProt (P0CX55) Pfam (PF00416) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
14 | AA, BA (C9, c9) | 40S ribosomal protein S19-A | polymer | 143 | 15810.9 | 2 | UniProt (P07280) Pfam (PF01090) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP55A,S16a,YP45,YS16A |
15 | CA, DA (d0, D0) | 40S ribosomal protein S20 | polymer | 107 | 12190.2 | 2 | UniProt (P38701) Pfam (PF00338) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
16 | EA, FA (d1, D1) | 40S ribosomal protein S21-A | polymer | 87 | 9758.8 | 2 | UniProt (P0C0V8) Pfam (PF01249) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S26,YS25 |
17 | GA, HA (d2, D2) | 40S ribosomal protein S22-A | polymer | 129 | 14518.9 | 2 | UniProt (P0C0W1) Pfam (PF00410) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50,S24,YP58,YS22 |
18 | IA, JA (d3, D3) | 40S ribosomal protein S23-A | polymer | 144 | 15942.7 | 2 | UniProt (P0CX29) Pfam (PF00164) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP37,S28,YS14 |
19 | KA, LA (d4, D4) | 40S ribosomal protein S24-A | polymer | 134 | 15231.6 | 2 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50 |
20 | MA, NA (d5, D5) | 40S ribosomal protein S25-A | polymer | 70 | 8001.4 | 2 | UniProt (Q3E792) Pfam (PF03297) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP45,S31,YS23 |
21 | OA, PA (d6, D6) | 40S ribosomal protein S26-B | polymer | 97 | 11023.0 | 2 | UniProt (P39939) Pfam (PF01283) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
22 | QA, RA (d7, D7) | 40S ribosomal protein S27-A | polymer | 81 | 8762.2 | 2 | UniProt (P35997) Pfam (PF01667) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61,YS20 |
23 | SA, TA (d8, D8) | 40S ribosomal protein S28-A | polymer | 63 | 7116.3 | 2 | UniProt (Q3E7X9) Pfam (PF01200) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S33,YS27 |
24 | UA, VA (d9, D9) | 40S ribosomal protein S29-A | polymer | 53 | 6335.3 | 2 | UniProt (P41057) Pfam (PF00253) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S36,YS29 |
25 | WA, XA (e0, E0) | 40S ribosomal protein S30-A | polymer | 61 | 6878.2 | 2 | UniProt (P0CX33) Pfam (PF04758) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
26 | YA, ZA (e1, E1) | Ubiquitin-40S ribosomal protein S31 | polymer | 73 | 8388.0 | 2 | UniProt (P05759) Pfam (PF01599) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
27 | AB, BB (l2, L2) | 60S ribosomal protein L2-A | polymer | 252 | 27217.3 | 2 | UniProt (P0CX45) Pfam (PF03947) Pfam (PF00181) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L5,RP8,YL6 |
28 | CB, DB (l3, L3) | 60S ribosomal protein L3 | polymer | 386 | 43719.6 | 2 | UniProt (P14126) Pfam (PF00297) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
29 | EB, FB (l4, L4) | 60S ribosomal protein L4-A | polymer | 361 | 39027.9 | 2 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L2,RP2,YL2 |
30 | GB, HB (l5, L5) | 60S ribosomal protein L5 | polymer | 296 | 33633.6 | 2 | UniProt (P26321) Pfam (PF14204) Pfam (PF17144) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L1,L1a,Ribosomal 5S RNA-binding protein,YL3 |
31 | IB, JB (l6, L6) | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 2 | UniProt (Q02326) Pfam (PF01159) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L17,RP18,YL16 |
32 | KB, LB (l7, L7) | 60S ribosomal protein L7-A | polymer | 223 | 25341.5 | 2 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L6,RP11,YL8 |
33 | MB, NB (l8, L8) | 60S ribosomal protein L8-A | polymer | 233 | 25815.0 | 2 | UniProt (P17076) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5 |
34 | OB, PB (l9, L9) | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 2 | UniProt (P05738) Pfam (PF00347) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L8,RP24,YL11 |
35 | QB, RB (m0, M0) | 60S ribosomal protein L10 | polymer | 221 | 25410.5 | 2 | UniProt (P41805) Pfam (PF00252) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
36 | SB, TB (m1, M1) | 60S ribosomal protein L11-B | polymer | 169 | 19266.1 | 2 | UniProt (Q3E757) Pfam (PF00281) Pfam (PF00673) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L16,RP39,YL22 |
37 | UB, VB (m3, M3) | 60S ribosomal protein L13-A | polymer | 194 | 21956.3 | 2 | UniProt (Q12690) Pfam (PF01294) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
38 | WB, XB (m4, M4) | 60S ribosomal protein L14-A | polymer | 137 | 15063.9 | 2 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
39 | YB, ZB (m5, M5) | 60S ribosomal protein L15-A | polymer | 203 | 24351.2 | 2 | UniProt (P05748) Pfam (PF00827) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L13,RP15R,YL10,YP18 |
40 | AC, BC (m6, M6) | 60S ribosomal protein L16-A | polymer | 197 | 22029.0 | 2 | UniProt (P26784) Pfam (PF00572) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L13a,L21,RP22,YL15 |
41 | CC, DC (m7, M7) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 2 | UniProt (P05740) Pfam (PF00237) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L20A,YL17 |
42 | EC, FC (m8, M8) | 60S ribosomal protein L18-A | polymer | 185 | 20478.1 | 2 | UniProt (P0CX49) Pfam (PF17135) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP28 |
43 | GC, HC (m9, M9) | 60S ribosomal protein L19-A | polymer | 188 | 21631.1 | 2 | UniProt (P0CX82) Pfam (PF01280) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L23,RP15L,RP33,YL14 |
44 | IC, JC (n0, N0) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 2 | UniProt (P0CX23) Pfam (PF01775) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L18a |
45 | KC, LC (n1, N1) | 60S ribosomal protein L21-A | polymer | 159 | 18148.1 | 2 | UniProt (Q02753) Pfam (PF01157) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
46 | MC, NC (n2, N2) | 60S ribosomal protein L22-A | polymer | 100 | 11263.9 | 2 | UniProt (P05749) Pfam (PF01776) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L1c,RP4,YL31 |
47 | OC, PC (n3, N3) | 60S ribosomal protein L23-A | polymer | 136 | 14362.8 | 2 | UniProt (P0CX41) Pfam (PF00238) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L17a,YL32 |
48 | QC, RC (n4, N4) | 60S ribosomal protein L24-A | polymer | 155 | 17661.7 | 2 | UniProt (P04449) Pfam (PF01246) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L30,RP29,YL21 |
49 | SC, TC (n5, N5) | 60S ribosomal protein L25 | polymer | 121 | 13771.2 | 2 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP16L,YL25,YP42' |
50 | UC, VC (n6, N6) | 60S ribosomal protein L26-A | polymer | 126 | 14134.6 | 2 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L33,YL33 |
51 | WC, XC (n7, N7) | 60S ribosomal protein L27-A | polymer | 135 | 15437.2 | 2 | UniProt (P0C2H6) Pfam (PF01777) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
52 | YC, ZC (n8, N8) | 60S ribosomal protein L28 | polymer | 148 | 16630.5 | 2 | UniProt (P02406) Pfam (PF00828) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L27a,L29,RP44,RP62,YL24 |
53 | AD, BD (n9, N9) | 60S ribosomal protein L29 | polymer | 58 | 6560.7 | 2 | UniProt (P05747) Pfam (PF01779) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | YL43 |
54 | CD, DD (o0, O0) | 60S ribosomal protein L30 | polymer | 100 | 10902.7 | 2 | UniProt (P14120) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L32,RP73,YL38 |
55 | ED, FD (o1, O1) | 60S ribosomal protein L31-A | polymer | 109 | 12649.8 | 2 | UniProt (P0C2H8) Pfam (PF01198) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L34,YL28 |
56 | GD, HD (o2, O2) | 60S ribosomal protein L32 | polymer | 127 | 14478.1 | 2 | UniProt (P38061) Pfam (PF01655) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
57 | ID, JD (o3, O3) | 60S ribosomal protein L33-A | polymer | 106 | 12045.9 | 2 | UniProt (P05744) Pfam (PF01247) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L37,RP47,YL37 |
58 | KD, LD (o4, O4) | 60S ribosomal protein L34-A | polymer | 112 | 12608.8 | 2 | UniProt (P87262) Pfam (PF01199) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
59 | MD, ND (o5, O5) | 60S ribosomal protein L35-A | polymer | 119 | 13811.4 | 2 | UniProt (P0CX84) Pfam (PF00831) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
60 | OD, PD (o6, O6) | 60S ribosomal protein L36-A | polymer | 99 | 11020.1 | 2 | UniProt (P05745) Pfam (PF01158) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L39,YL39 |
61 | QD, RD (o7, O7) | 60S ribosomal protein L37-A | polymer | 87 | 9746.2 | 2 | UniProt (P49166) Pfam (PF01907) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L43,YL35,YP55 |
62 | SD, TD (o8, O8) | 60S ribosomal protein L38 | polymer | 77 | 8714.4 | 2 | UniProt (P49167) Pfam (PF01781) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
63 | UD, VD (o9, O9) | 60S ribosomal protein L39 | polymer | 50 | 6227.4 | 2 | UniProt (P04650) Pfam (PF00832) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L46,YL40 |
64 | WD, XD (q0, Q0) | Ubiquitin-60S ribosomal protein L40 | polymer | 52 | 6032.3 | 2 | UniProt (P0CH08) Pfam (PF01020) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
65 | YD, ZD (q1, Q1) | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 2 | UniProt (P0CX86) Pfam (PF05162) | Saccharomyces cerevisiae (Baker's yeast) | L47,YL41 |
66 | AE, BE (q2, Q2) | 60S ribosomal protein L42-A | polymer | 105 | 12115.5 | 2 | UniProt (P0CX27) Pfam (PF00935) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L41,YL27,YP44 |
67 | CE, DE (q3, Q3) | 60S ribosomal protein L43-A | polymer | 91 | 9981.8 | 2 | UniProt (P0CX25) Pfam (PF01780) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L37a,YL35 |
68 | EE, FE (S0, s0) | 40S ribosomal protein S0-A | polymer | 206 | 22811.1 | 2 | UniProt (P32905) Pfam (PF00318) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nucleic acid-binding protein NAB1A |
69 | GE, HE (S1, s1) | 40S ribosomal protein S1-A | polymer | 216 | 24498.4 | 2 | UniProt (P33442) Pfam (PF01015) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP10A |
70 | IE, JE (S2, s2) | 40S ribosomal protein S2 | polymer | 217 | 23213.0 | 2 | UniProt (P25443) Pfam (PF00333) Pfam (PF03719) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Omnipotent suppressor protein SUP44,RP12,S4,YS5 |
71 | KE, LE (S3, s3) | 40S ribosomal protein S3 | polymer | 223 | 24702.8 | 2 | UniProt (P05750) Pfam (PF07650) Pfam (PF00189) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP13,YS3 |
72 | ME, NE (S4, s4) | 40S ribosomal protein S4-A | polymer | 260 | 29338.1 | 2 | UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP5,S7,YS6 |
73 | OE, PE (S5, s5) | 40S ribosomal protein S5 | polymer | 206 | 22908.3 | 2 | UniProt (P26783) Pfam (PF00177) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP14,S2,YS8 |
74 | QE, RE (S6, s6) | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 2 | UniProt (P0CX37) Pfam (PF01092) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP9,S10,YS4 |
75 | SE, TE (s7, S7) | 40S ribosomal protein S7-A | polymer | 184 | 21000.5 | 2 | UniProt (P26786) Pfam (PF01251) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP30,RP40 |
76 | UE, VE (s8, S8) | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 2 | UniProt (P0CX39) Pfam (PF01201) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP19,S14,YS9 |
77 | WE, XE (S9, s9) | 40S ribosomal protein S9-A | polymer | 185 | 21210.7 | 2 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP21,S13,YP28,YS11 |
78 | YE, ZE (sM, SM) | Suppressor protein STM1 | polymer | 272 | 29916.8 | 2 | UniProt (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 |
79 | AF, BF (sR, SR) | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 318 | 34710.0 | 2 | UniProt (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 |
80 | AAA, AAB, ABA, ABB, ACA... (2, 6, c1, 4, L2...) | MAGNESIUM ION | non-polymer | 24.3 | 1365 | Chemie (MG) | |||
81 | AWA, AY, BDA, BY, CDA... (5, 1, 2, 6, 4...) | TC007 | non-polymer | 483.5 | 25 | Chemie (8UZ) | |||
82 | AGB, CGB, GGB, JGB, MGB... (o4, O4, o7, O7, q0...) | ZINC ION | non-polymer | 65.4 | 17 | Chemie (ZN) | |||
83 | AIB, AJB, BIB, BJB, CIB... (D6, N6, d9, n8, l2...) | 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 |