5NDG
Crystal structure of geneticin (G418) 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, BC (2, 6) | 18S ribosomal RNA | polymer | 1800 | 579761.9 | 2 | GenBank (874346701) | Saccharomyces cerevisiae (Baker's yeast) | |
| 2 | B, CC (S0, s0) | 40S ribosomal protein S0-A | polymer | 206 | 22811.1 | 2 | UniProt (P32905) Pfam (PF00318) | Saccharomyces cerevisiae (Baker's yeast) | Nucleic acid-binding protein NAB1A |
| 3 | C, DC (S1, s1) | 40S ribosomal protein S1-A | polymer | 216 | 24498.4 | 2 | UniProt (P33442) Pfam (PF01015) | Saccharomyces cerevisiae (Baker's yeast) | RP10A |
| 4 | D, EC (S2, s2) | 40S ribosomal protein S2 | polymer | 217 | 23213.0 | 2 | UniProt (P25443) Pfam (PF00333) Pfam (PF03719) | Saccharomyces cerevisiae (Baker's yeast) | Omnipotent suppressor protein SUP44,RP12,S4,YS5 |
| 5 | E, FC (S3, s3) | 40S ribosomal protein S3 | polymer | 223 | 24702.8 | 2 | UniProt (P05750) Pfam (PF07650) Pfam (PF00189) | Saccharomyces cerevisiae (Baker's yeast) | RP13,YS3 |
| 6 | F, GC (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 (Baker's yeast) | RP5,S7,YS6 |
| 7 | G, HC (S5, s5) | 40S ribosomal protein S5 | polymer | 206 | 22908.3 | 2 | UniProt (P26783) Pfam (PF00177) | Saccharomyces cerevisiae (Baker's yeast) | RP14,S2,YS8 |
| 8 | H, IC (S6, s6) | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 2 | UniProt (P0CX37) Pfam (PF01092) | Saccharomyces cerevisiae (Baker's yeast) | RP9,S10,YS4 |
| 9 | I, JC (S7, s7) | 40S ribosomal protein S7-A | polymer | 185 | 21071.6 | 2 | UniProt (P26786) Pfam (PF01251) | Saccharomyces cerevisiae (Baker's yeast) | RP30,RP40 |
| 10 | J, KC (S8, s8) | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 2 | UniProt (P0CX39) Pfam (PF01201) | Saccharomyces cerevisiae (Baker's yeast) | RP19,S14,YS9 |
| 11 | K, LC (S9, s9) | 40S ribosomal protein S9-A | polymer | 185 | 21210.7 | 2 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) | Saccharomyces cerevisiae (Baker's yeast) | RP21,S13,YP28,YS11 |
| 12 | L, MC (C0, c0) | 40S ribosomal protein S10-A | polymer | 105 | 12757.4 | 2 | UniProt (Q08745) Pfam (PF03501) | Saccharomyces cerevisiae (Baker's yeast) | |
| 13 | M, NC (C1, c1) | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 2 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) | Saccharomyces cerevisiae (Baker's yeast) | RP41,S18,YS12 |
| 14 | N, OC (C2, c2) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 2 | UniProt (P48589) Pfam (PF01248) | Saccharomyces cerevisiae (Baker's yeast) | |
| 15 | O, PC (C3, c3) | 40S ribosomal protein S13 | polymer | 150 | 16928.7 | 2 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) | Saccharomyces cerevisiae (Baker's yeast) | S27a,YS15 |
| 16 | P, QC (C4, c4) | 40S ribosomal protein S14-A | polymer | 128 | 13560.5 | 2 | UniProt (P06367) Pfam (PF00411) | Saccharomyces cerevisiae (Baker's yeast) | RP59A |
| 17 | Q, RC (C5, c5) | 40S ribosomal protein S15 | polymer | 141 | 15900.7 | 2 | UniProt (Q01855) Pfam (PF00203) | Saccharomyces cerevisiae (Baker's yeast) | RIG protein,RP52,S21,YS21 |
| 18 | R, SC (C6, c6) | 40S ribosomal protein S16-A | polymer | 141 | 15659.2 | 2 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae (Baker's yeast) | RP61R |
| 19 | S, TC (C7, c7) | 40S ribosomal protein S17-A | polymer | 136 | 15820.4 | 2 | UniProt (P02407) Pfam (PF00833) | Saccharomyces cerevisiae (Baker's yeast) | RP51A |
| 20 | T, UC (C8, c8) | 40S ribosomal protein S18-A | polymer | 145 | 16940.4 | 2 | UniProt (P0CX55) Pfam (PF00416) | Saccharomyces cerevisiae (Baker's yeast) | |
| 21 | U, VC (C9, c9) | 40S ribosomal protein S19-A | polymer | 143 | 15810.9 | 2 | UniProt (P07280) Pfam (PF01090) | Saccharomyces cerevisiae (Baker's yeast) | RP55A,S16a,YP45,YS16A |
| 22 | V, WC (D0, d0) | 40S ribosomal protein S20 | polymer | 107 | 12190.2 | 2 | UniProt (P38701) Pfam (PF00338) | Saccharomyces cerevisiae (Baker's yeast) | |
| 23 | W, XC (D1, d1) | 40S ribosomal protein S21-A | polymer | 87 | 9758.8 | 2 | UniProt (P0C0V8) Pfam (PF01249) | Saccharomyces cerevisiae (Baker's yeast) | S26,YS25 |
| 24 | X, YC (D2, d2) | 40S ribosomal protein S22-A | polymer | 129 | 14518.9 | 2 | UniProt (P0C0W1) Pfam (PF00410) | Saccharomyces cerevisiae (Baker's yeast) | RP50,S24,YP58,YS22 |
| 25 | Y, ZC (D3, d3) | 40S ribosomal protein S23-A | polymer | 144 | 15942.7 | 2 | UniProt (P0CX29) Pfam (PF00164) | Saccharomyces cerevisiae (Baker's yeast) | RP37,S28,YS14 |
| 26 | AD, Z (D4, d4) | 40S ribosomal protein S24-A | polymer | 134 | 15231.6 | 2 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae (Baker's yeast) | RP50 |
| 27 | AA, BD (D5, d5) | 40S ribosomal protein S25-A | polymer | 70 | 8001.4 | 2 | UniProt (Q3E792) Pfam (PF03297) | Saccharomyces cerevisiae (Baker's yeast) | RP45,S31,YS23 |
| 28 | BA, CD (D6, d6) | 40S ribosomal protein S26-B | polymer | 97 | 11023.0 | 2 | UniProt (P39939) Pfam (PF01283) | Saccharomyces cerevisiae (Baker's yeast) | |
| 29 | CA, DD (D7, d7) | 40S ribosomal protein S27-A | polymer | 81 | 8762.2 | 2 | UniProt (P35997) Pfam (PF01667) | Saccharomyces cerevisiae (Baker's yeast) | RP61,YS20 |
| 30 | DA, ED (D8, d8) | 40S ribosomal protein S28-A | polymer | 63 | 7116.3 | 2 | UniProt (Q3E7X9) Pfam (PF01200) | Saccharomyces cerevisiae (Baker's yeast) | S33,YS27 |
| 31 | EA, FD (D9, d9) | 40S ribosomal protein S29-A | polymer | 53 | 6335.3 | 2 | UniProt (P41057) Pfam (PF00253) | Saccharomyces cerevisiae (Baker's yeast) | S36,YS29 |
| 32 | FA, GD (E0, e0) | 40S ribosomal protein S30-A | polymer | 60 | 6779.1 | 2 | UniProt (P0CX33) Pfam (PF04758) | Saccharomyces cerevisiae (Baker's yeast) | |
| 33 | GA, HD (E1, e1) | Ubiquitin-40S ribosomal protein S31 | polymer | 152 | 17254.2 | 2 | UniProt (P05759) Pfam (PF00240) Pfam (PF01599) | Saccharomyces cerevisiae (Baker's yeast) | |
| 34 | HA, ID (SR, sR) | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 318 | 34651.9 | 2 | UniProt (P38011) Pfam (PF00400) | Saccharomyces cerevisiae (Baker's yeast) | Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1 |
| 35 | IA, JD (SM, sM) | Suppressor protein STM1 | polymer | 272 | 29916.8 | 2 | UniProt (P39015) Pfam (PF09598) | Saccharomyces cerevisiae (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 |
| 36 | JA, KD (1, 5) | 25S ribosomal RNA | polymer | 3396 | 1097493.9 | 2 | GenBank (834774822) | Saccharomyces cerevisiae (Baker's yeast) | |
| 37 | KA, LD (3, 7) | 5S ribosomal RNA | polymer | 121 | 38951.1 | 2 | GenBank (1039024062) | Saccharomyces cerevisiae (Baker's yeast) | |
| 38 | LA, MD (4, 8) | 5.8S ribosomal RNA | polymer | 158 | 50682.9 | 2 | GenBank (1102645687) | Saccharomyces cerevisiae (Baker's yeast) | |
| 39 | MA, ND (L2, l2) | 60S ribosomal protein L2-A | polymer | 252 | 27217.3 | 2 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) | Saccharomyces cerevisiae (Baker's yeast) | L5,RP8,YL6 |
| 40 | NA, OD (L3, l3) | 60S ribosomal protein L3 | polymer | 386 | 43719.6 | 2 | UniProt (P14126) Pfam (PF00297) | Saccharomyces cerevisiae (Baker's yeast) | Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 41 | OA, PD (L4, l4) | 60S ribosomal protein L4-A | polymer | 361 | 39027.9 | 2 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) | Saccharomyces cerevisiae (Baker's yeast) | L2,RP2,YL2 |
| 42 | PA, QD (L5, l5) | 60S ribosomal protein L5 | polymer | 296 | 33633.6 | 2 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) | Saccharomyces cerevisiae (Baker's yeast) | L1,L1a,Ribosomal 5S RNA-binding protein,YL3 |
| 43 | QA, RD (L6, l6) | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 2 | UniProt (Q02326) Pfam (PF01159) | Saccharomyces cerevisiae (Baker's yeast) | L17,RP18,YL16 |
| 44 | RA, SD (L7, l7) | 60S ribosomal protein L7-A | polymer | 223 | 25341.5 | 2 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) | Saccharomyces cerevisiae (Baker's yeast) | L6,RP11,YL8 |
| 45 | SA, TD (L8, l8) | 60S ribosomal protein L8-A | polymer | 233 | 25815.0 | 2 | UniProt (P17076) Pfam (PF01248) | Saccharomyces cerevisiae (Baker's yeast) | L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5 |
| 46 | TA, UD (L9, l9) | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 2 | UniProt (P05738) Pfam (PF00347) | Saccharomyces cerevisiae (Baker's yeast) | L8,RP24,YL11 |
| 47 | UA, VD (M0, m0) | 60S ribosomal protein L10 | polymer | 221 | 25410.5 | 2 | UniProt (P41805) Pfam (PF00252) | Saccharomyces cerevisiae (Baker's yeast) | L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
| 48 | VA, WD (M1, m1) | 60S ribosomal protein L11-A | polymer | 169 | 19266.1 | 2 | UniProt (P0C0W9) Pfam (PF00281) Pfam (PF00673) | Saccharomyces cerevisiae (Baker's yeast) | L16,RP39,YL22 |
| 49 | WA, XD (M3, m3) | 60S ribosomal protein L13-A | polymer | 194 | 21956.3 | 2 | UniProt (Q12690) Pfam (PF01294) | Saccharomyces cerevisiae (Baker's yeast) | |
| 50 | XA, YD (M4, m4) | 60S ribosomal protein L14-A | polymer | 137 | 15063.9 | 2 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) | Saccharomyces cerevisiae (Baker's yeast) | |
| 51 | YA, ZD (M5, m5) | 60S ribosomal protein L15-A | polymer | 203 | 24351.2 | 2 | UniProt (P05748) Pfam (PF00827) | Saccharomyces cerevisiae (Baker's yeast) | L13,RP15R,YL10,YP18 |
| 52 | AE, ZA (M6, m6) | 60S ribosomal protein L16-A | polymer | 197 | 22029.0 | 2 | UniProt (P26784) Pfam (PF00572) | Saccharomyces cerevisiae (Baker's yeast) | L13a,L21,RP22,YL15 |
| 53 | AB, BE (M7, m7) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 2 | UniProt (P05740) Pfam (PF00237) | Saccharomyces cerevisiae (Baker's yeast) | L20A,YL17 |
| 54 | BB, CE (M8, m8) | 60S ribosomal protein L18-A | polymer | 185 | 20478.1 | 2 | UniProt (P0CX49) Pfam (PF17135) | Saccharomyces cerevisiae (Baker's yeast) | RP28 |
| 55 | CB, DE (M9, m9) | 60S ribosomal protein L19-A | polymer | 188 | 21631.1 | 2 | UniProt (P0CX82) Pfam (PF01280) | Saccharomyces cerevisiae (Baker's yeast) | L23,RP15L,RP33,YL14 |
| 56 | DB, EE (N0, n0) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 2 | UniProt (P0CX23) Pfam (PF01775) | Saccharomyces cerevisiae (Baker's yeast) | L18a |
| 57 | EB, FE (N1, n1) | 60S ribosomal protein L21-A | polymer | 159 | 18148.1 | 2 | UniProt (Q02753) Pfam (PF01157) | Saccharomyces cerevisiae (Baker's yeast) | |
| 58 | FB, GE (N2, n2) | 60S ribosomal protein L22-A | polymer | 98 | 11006.6 | 2 | UniProt (P05749) Pfam (PF01776) | Saccharomyces cerevisiae (Baker's yeast) | L1c,RP4,YL31 |
| 59 | GB, HE (N3, n3) | 60S ribosomal protein L23-A | polymer | 135 | 14275.7 | 2 | UniProt (P0CX41) Pfam (PF00238) | Saccharomyces cerevisiae (Baker's yeast) | L17a,YL32 |
| 60 | HB, IE (N4, n4) | 60S ribosomal protein L24-A | polymer | 155 | 17661.7 | 2 | UniProt (P04449) Pfam (PF01246) | Saccharomyces cerevisiae (Baker's yeast) | L30,RP29,YL21 |
| 61 | IB, JE (N5, n5) | 60S ribosomal protein L25 | polymer | 121 | 13771.2 | 2 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) | Saccharomyces cerevisiae (Baker's yeast) | RP16L,YL25,YP42' |
| 62 | JB, KE (N6, n6) | 60S ribosomal protein L26-A | polymer | 126 | 14134.6 | 2 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) | Saccharomyces cerevisiae (Baker's yeast) | L33,YL33 |
| 63 | KB, LE (N7, n7) | 60S ribosomal protein L27-A | polymer | 135 | 15437.2 | 2 | UniProt (P0C2H6) Pfam (PF01777) | Saccharomyces cerevisiae (Baker's yeast) | |
| 64 | LB, ME (N8, n8) | 60S ribosomal protein L28 | polymer | 148 | 16630.5 | 2 | UniProt (P02406) Pfam (PF00828) | Saccharomyces cerevisiae (Baker's yeast) | L27a,L29,RP44,RP62,YL24 |
| 65 | MB, NE (N9, n9) | 60S ribosomal protein L29 | polymer | 58 | 6560.7 | 2 | UniProt (P05747) Pfam (PF01779) | Saccharomyces cerevisiae (Baker's yeast) | YL43 |
| 66 | NB, OE (O0, o0) | 60S ribosomal protein L30 | polymer | 100 | 10902.7 | 2 | UniProt (P14120) Pfam (PF01248) | Saccharomyces cerevisiae (Baker's yeast) | L32,RP73,YL38 |
| 67 | OB, PE (O1, o1) | 60S ribosomal protein L31-A | polymer | 109 | 12649.8 | 2 | UniProt (P0C2H8) Pfam (PF01198) | Saccharomyces cerevisiae (Baker's yeast) | L34,YL28 |
| 68 | PB, QE (O2, o2) | 60S ribosomal protein L32 | polymer | 127 | 14478.1 | 2 | UniProt (P38061) Pfam (PF01655) | Saccharomyces cerevisiae (Baker's yeast) | |
| 69 | QB, RE (O3, o3) | 60S ribosomal protein L33-A | polymer | 106 | 12045.9 | 2 | UniProt (P05744) Pfam (PF01247) | Saccharomyces cerevisiae (Baker's yeast) | L37,RP47,YL37 |
| 70 | RB, SE (O4, o4) | 60S ribosomal protein L34-A | polymer | 112 | 12608.8 | 2 | UniProt (P87262) Pfam (PF01199) | Saccharomyces cerevisiae (Baker's yeast) | |
| 71 | SB, TE (O5, o5) | 60S ribosomal protein L35-A | polymer | 119 | 13811.4 | 2 | UniProt (P0CX84) Pfam (PF00831) | Saccharomyces cerevisiae (Baker's yeast) | |
| 72 | TB, UE (O6, o6) | 60S ribosomal protein L36-A | polymer | 99 | 11020.1 | 2 | UniProt (P05745) Pfam (PF01158) | Saccharomyces cerevisiae (Baker's yeast) | L39,YL39 |
| 73 | UB, VE (O7, o7) | 60S ribosomal protein L37-A | polymer | 84 | 9517.0 | 2 | UniProt (P49166) Pfam (PF01907) | Saccharomyces cerevisiae (Baker's yeast) | L43,YL35,YP55 |
| 74 | VB, WE (O8, o8) | 60S ribosomal protein L38 | polymer | 77 | 8714.4 | 2 | UniProt (P49167) Pfam (PF01781) | Saccharomyces cerevisiae (Baker's yeast) | |
| 75 | WB, XE (O9, o9) | 60S ribosomal protein L39 | polymer | 50 | 6227.4 | 2 | UniProt (P04650) Pfam (PF00832) | Saccharomyces cerevisiae (Baker's yeast) | L46,YL40 |
| 76 | XB, YE (Q0, q0) | Ubiquitin-60S ribosomal protein L40 | polymer | 52 | 6032.3 | 2 | UniProt (P0CH08) Pfam (PF01020) | Saccharomyces cerevisiae (Baker's yeast) | |
| 77 | YB, ZE (Q1, q1) | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 2 | UniProt (P0CX86) Pfam (PF05162) | Saccharomyces cerevisiae (Baker's yeast) | L47,YL41 |
| 78 | AF, ZB (Q2, q2) | 60S ribosomal protein L42-A | polymer | 105 | 12115.5 | 2 | UniProt (P0CX27) Pfam (PF00935) | Saccharomyces cerevisiae (Baker's yeast) | L41,YL27,YP44 |
| 79 | AC, BF (Q3, q3) | 60S ribosomal protein L43-A | polymer | 91 | 9981.8 | 2 | UniProt (P0CX25) Pfam (PF01780) | Saccharomyces cerevisiae (Baker's yeast) | L37a,YL35 |
| 80 | CF (p0) | 60S acidic ribosomal protein P0 | polymer | 312 | 33749.1 | 1 | UniProt (P05317) Pfam (PF00466) Pfam (PF17777) Pfam (PF00428) | Saccharomyces cerevisiae (Baker's yeast) | A0,L10E |
| 81 | AAA, AAB, ABA, ACA, ADA... (3, l3, 4, N7, 6...) | MAGNESIUM ION | non-polymer | 24.3 | 1221 | Chemie (MG) | |||
| 82 | CHA, DHA, EHA, KJ, LJ... (6, 2, 5, 1, n6) | GENETICIN | non-polymer | 496.6 | 21 | Chemie (GET) | |||
| 83 | ABB, CBB, IBB, ICA, JBB... (o4, o7, q0, O4, q2...) | ZINC ION | non-polymer | 65.4 | 18 | Chemie (ZN) | |||
| 84 | ACB, ADB, BCB, BDB, CCB... (4, m0, L2, m5, L3...) | water | water | 18.0 | 1054 | Chemie (HOH) |
Sequence modifications
SR, sR: 2 - 319 (UniProt: P38011)
| PDB | External Database | Details |
|---|---|---|
| Ala 161 | Lys 161 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 159 |
| Total formula weight | 6191892.7 | |
| Non-Polymers* | Number of molecules | 1260 |
| Total formula weight | 41281.4 | |
| All* | Total formula weight | 6233174.1 |
