5IB7
Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin
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, EB (13, 1G) | 16S ribosomal RNA | polymer | 1522 | 493997.3 | 2 | GenBank (55771382) | Thermus thermophilus HB8 | |
| 2 | B, FB (1E, 12) | 30S ribosomal protein S2 | polymer | 256 | 29317.7 | 2 | UniProt (P80371) Pfam (PF00318) | Thermus thermophilus HB8 | |
| 3 | C, GB (2E, 22) | 30S ribosomal protein S3 | polymer | 239 | 26751.1 | 2 | UniProt (P80372) Pfam (PF07650) Pfam (PF00189) | Thermus thermophilus HB8 | |
| 4 | D, HB (3E, 32) | 30S ribosomal protein S4 | polymer | 209 | 24373.4 | 2 | UniProt (P80373) Pfam (PF00163) Pfam (PF01479) | Thermus thermophilus HB8 | |
| 5 | E, IB (4E, 42) | 30S ribosomal protein S5 | polymer | 162 | 17583.4 | 2 | UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) | Thermus thermophilus HB8 | |
| 6 | F, JB (5E, 52) | 30S ribosomal protein S6 | polymer | 101 | 11988.8 | 2 | UniProt (Q5SLP8) Pfam (PF01250) | Thermus thermophilus HB8 | TS9 |
| 7 | G, KB (6E, 62) | 30S ribosomal protein S7 | polymer | 156 | 18051.0 | 2 | UniProt (P17291) Pfam (PF00177) | Thermus thermophilus HB8 | |
| 8 | H, LB (7E, 72) | 30S ribosomal protein S8 | polymer | 138 | 15868.6 | 2 | UniProt (Q5SHQ2) Pfam (PF00410) UniProt (by SIFTS) (P0DOY9) | Thermus thermophilus HB8 | |
| 9 | I, MB (8E, 82) | 30S ribosomal protein S9 | polymer | 128 | 14410.6 | 2 | UniProt (P80374) Pfam (PF00380) | Thermus thermophilus HB8 | |
| 10 | J, NB (1I, 1A) | 30S ribosomal protein S10 | polymer | 105 | 11955.0 | 2 | UniProt (Q5SHN7) Pfam (PF00338) | Thermus thermophilus HB8 | |
| 11 | K, OB (2I, 2A) | 30S ribosomal protein S11 | polymer | 129 | 13737.9 | 2 | UniProt (P80376) Pfam (PF00411) | Thermus thermophilus HB8 | |
| 12 | L, PB (3I, 3A) | 30S ribosomal protein S12 | polymer | 132 | 14637.4 | 2 | UniProt (Q5SHN3) Pfam (PF00164) | Thermus thermophilus HB8 | |
| 13 | M, QB (4I, 4A) | 30S ribosomal protein S13 | polymer | 126 | 14338.9 | 2 | UniProt (P80377) Pfam (PF00416) | Thermus thermophilus HB8 | |
| 14 | N, RB (5I, 5A) | 30S ribosomal protein S14 type Z | polymer | 61 | 7158.7 | 2 | UniProt (Q5SHQ1) Pfam (PF00253) UniProt (by SIFTS) (P0DOY6) | Thermus thermophilus HB8 | |
| 15 | O, SB (6I, 6A) | 30S ribosomal protein S15 | polymer | 89 | 10578.4 | 2 | UniProt (Q5SJ76) Pfam (PF00312) | Thermus thermophilus HB8 | |
| 16 | P, TB (7I, 7A) | 30S ribosomal protein S16 | polymer | 88 | 10410.0 | 2 | UniProt (Q5SJH3) Pfam (PF00886) | Thermus thermophilus HB8 | |
| 17 | Q, UB (8I, 8A) | 30S ribosomal protein S17 | polymer | 105 | 12325.7 | 2 | UniProt (Q5SHP7) Pfam (PF00366) UniProt (by SIFTS) (P0DOY7) | Thermus thermophilus HB8 | |
| 18 | R, VB (9I, 9A) | 30S ribosomal protein S18 | polymer | 88 | 10258.3 | 2 | UniProt (Q5SLQ0) Pfam (PF01084) | Thermus thermophilus HB8 | |
| 19 | S, WB (AI, AA) | 30S ribosomal protein S19 | polymer | 93 | 10605.5 | 2 | UniProt (Q5SHP2) Pfam (PF00203) | Thermus thermophilus HB8 | |
| 20 | T, XB (BI, BA) | 30S ribosomal protein S20 | polymer | 106 | 11736.1 | 2 | UniProt (P80380) Pfam (PF01649) | Thermus thermophilus HB8 | |
| 21 | U, YB (1F, 1B) | 30S ribosomal protein Thx | polymer | 27 | 3350.0 | 2 | UniProt (Q5SIH3) Pfam (PF17070) | Thermus thermophilus HB8 | S31 |
| 22 | V (1K) | tRNALys | polymer | 76 | 24596.7 | 1 | Escherichia coli K-12 | ||
| 23 | AC, W (2K, 2L) | tRNAfMet | polymer | 77 | 24862.0 | 2 | Escherichia coli K-12 | ||
| 24 | BC, X, ZB (3K, 1L, 3L) | tRNALys | polymer | 76 | 24378.4 | 3 | Escherichia coli K-12 | ||
| 25 | CC, Y (4K, 4L) | mRNA | polymer | 30 | 9889.1 | 2 | Escherichia coli | ||
| 26 | DC, Z (1H, 14) | 23S ribosomal RNA | polymer | 2917 | 948539.9 | 2 | GenBank (55771382) | Thermus thermophilus HB8 | |
| 27 | AA, EC (16, 1J) | 5S ribosomal RNA | polymer | 122 | 39540.6 | 2 | GenBank (55771382) | Thermus thermophilus HB8 | |
| 28 | BA (71) | 50S ribosomal protein L1 | polymer | 229 | 24867.7 | 1 | UniProt (P27150) | Thermus thermophilus HB8 | |
| 29 | CA, FC (11, 19) | 50S ribosomal protein L2 | polymer | 276 | 30532.6 | 2 | UniProt (P60405) Pfam (PF00181) Pfam (PF03947) | Thermus thermophilus HB8 | |
| 30 | DA, GC (21, 29) | 50S ribosomal protein L3 | polymer | 206 | 22450.2 | 2 | UniProt (Q5SHN8) Pfam (PF00297) | Thermus thermophilus HB8 | |
| 31 | EA, HC (31, 39) | 50S ribosomal protein L4 | polymer | 210 | 23271.9 | 2 | UniProt (Q5SHN9) Pfam (PF00573) | Thermus thermophilus HB8 | L1e |
| 32 | FA, IC (41, 49) | 50S ribosomal protein L5 | polymer | 182 | 21061.6 | 2 | UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) | Thermus thermophilus HB8 | |
| 33 | GA, JC (51, 59) | 50S ribosomal protein L6 | polymer | 180 | 19568.9 | 2 | UniProt (Q5SHQ3) Pfam (PF00347) UniProt (by SIFTS) (P0DOY8) | Thermus thermophilus HB8 | |
| 34 | HA, KC (61, 69) | 50S ribosomal protein L9 | polymer | 148 | 16422.2 | 2 | UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) | Thermus thermophilus HB8 | |
| 35 | IA, LC (58, 15) | 50S ribosomal protein L13 | polymer | 140 | 15927.9 | 2 | UniProt (P60488) Pfam (PF00572) | Thermus thermophilus HB8 | |
| 36 | JA, MC (68, 25) | 50S ribosomal protein L14 | polymer | 122 | 13323.6 | 2 | UniProt (Q5SHP8) Pfam (PF00238) | Thermus thermophilus HB8 | |
| 37 | KA, NC (78, 35) | 50S ribosomal protein L15 | polymer | 150 | 16319.1 | 2 | UniProt (Q5SHQ7) Pfam (PF00828) | Thermus thermophilus HB8 | |
| 38 | LA, OC (88, 45) | 50S ribosomal protein L16 | polymer | 141 | 15993.9 | 2 | UniProt (P60489) Pfam (PF00252) | Thermus thermophilus HB8 | |
| 39 | MA, PC (98, 55) | 50S ribosomal protein L17 | polymer | 118 | 13750.1 | 2 | UniProt (Q9Z9H5) Pfam (PF01196) | Thermus thermophilus HB8 | |
| 40 | NA, QC (A8, 65) | 50S ribosomal protein L18 | polymer | 112 | 12639.8 | 2 | UniProt (Q5SHQ4) Pfam (PF00861) | Thermus thermophilus HB8 | TL24 |
| 41 | OA, RC (B8, 75) | 50S ribosomal protein L19 | polymer | 146 | 17188.8 | 2 | UniProt (P60490) Pfam (PF01245) | Thermus thermophilus HB8 | |
| 42 | PA, SC (C8, 85) | 50S ribosomal protein L20 | polymer | 118 | 13779.3 | 2 | UniProt (P60491) Pfam (PF00453) | Thermus thermophilus HB8 | |
| 43 | QA, TC (D8, 95) | 50S ribosomal protein L21 | polymer | 101 | 11069.2 | 2 | UniProt (P60492) Pfam (PF00829) | Thermus thermophilus HB8 | |
| 44 | RA, UC (E8, A5) | 50S ribosomal protein L22 | polymer | 113 | 12808.1 | 2 | UniProt (Q5SHP3) Pfam (PF00237) | Thermus thermophilus HB8 | |
| 45 | SA, VC (F8, B5) | 50S ribosomal protein L23 | polymer | 96 | 10759.8 | 2 | UniProt (Q5SHP0) Pfam (PF00276) | Thermus thermophilus HB8 | |
| 46 | TA, WC (G8, C5) | 50S ribosomal protein L24 | polymer | 110 | 12085.6 | 2 | UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) | Thermus thermophilus HB8 | |
| 47 | UA, XC (H8, D5) | 50S ribosomal protein L25 | polymer | 206 | 23238.6 | 2 | UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) | Thermus thermophilus HB8 | TL5 |
| 48 | VA, YC (I8, E5) | 50S ribosomal protein L27 | polymer | 85 | 9529.1 | 2 | UniProt (P60493) Pfam (PF01016) | Thermus thermophilus HB8 | |
| 49 | WA, ZC (J8, F5) | 50S ribosomal protein L28 | polymer | 98 | 11004.2 | 2 | UniProt (P60494) Pfam (PF00830) | Thermus thermophilus HB8 | |
| 50 | AD, XA (K8, G5) | 50S ribosomal protein L29 | polymer | 72 | 8670.3 | 2 | UniProt (Q5SHP6) Pfam (PF00831) | Thermus thermophilus HB8 | |
| 51 | BD, YA (L8, H5) | 50S ribosomal protein L30 | polymer | 60 | 6799.1 | 2 | UniProt (Q5SHQ6) Pfam (PF00327) | Thermus thermophilus HB8 | |
| 52 | ZA (M8) | 50S ribosomal protein L31 | polymer | 71 | 8300.5 | 1 | UniProt (Q5SJE1) Pfam (PF01197) | Thermus thermophilus HB8 | |
| 53 | AB, CD (N8, J5) | 50S ribosomal protein L32 | polymer | 60 | 6722.1 | 2 | UniProt (P80339) Pfam (PF01783) | Thermus thermophilus HB8 | |
| 54 | BB (O8) | 50S ribosomal protein L33 | polymer | 54 | 6632.9 | 1 | UniProt (P35871) Pfam (PF00471) | Thermus thermophilus HB8 | |
| 55 | CB, DD (P8, L5) | 50S ribosomal protein L34 | polymer | 49 | 6132.4 | 2 | UniProt (P80340) Pfam (PF00468) | Thermus thermophilus HB8 | |
| 56 | DB, ED (Q8, M5) | 50S ribosomal protein L35 | polymer | 65 | 7506.2 | 2 | UniProt (Q5SKU1) Pfam (PF01632) | Thermus thermophilus HB8 | |
| 57 | AAA, ABA, ACA, ADA, AE... (1H, 13, P8, 1G, 14...) | MAGNESIUM ION | non-polymer | 24.3 | 1258 | Chemie (MG) PubChem (888) | |||
| 58 | PI, ZHA (13, 1G) | PAROMOMYCIN | non-polymer | 615.6 | 2 | Chemie (PAR) PubChem (16757804) PubChem (16760604) PubChem (17757254) PubChem (20849281) PubChem (71191297) PubChem (165580) PubChem (23789070) PubChem (24096964) PubChem (24867526) PubChem (24867858) PubChem (25104843) PubChem (71188564) PubChem (44120093) PubChem (44251565) PubChem (44186758) PubChem (44663324) PubChem (45358711) PubChem (53486370) PubChem (50989619) PubChem (58160567) PubChem (59361026) PubChem (59800245) PubChem (70793652) PubChem (70793824) PubChem (70795918) PubChem (71068776) PubChem (71072581) PubChem (71072592) PubChem (66932615) PubChem (68032118) PubChem (4689) PubChem (14951) PubChem (24176) PubChem (6602492) PubChem (6713982) PubChem (70878598) PubChem (71751432) PubChem (91151908) PubChem (73707499) PubChem (9961808) PubChem (3040200) PubChem (94469269) PubChem (94469270) PubChem (94469271) PubChem (91867972) PubChem (98048758) PubChem (98048760) PubChem (91972181) PubChem (94469268) PubChem (98048759) PubChem (98048761) PubChem (5702262) PubChem (121292209) PubChem (6603975) PubChem (101739930) PubChem (6604293) PubChem (122537356) PubChem (6710686) PubChem (124226135) PubChem (124464537) PubChem (9809147) PubChem (125040357) PubChem (125040359) PubChem (125121197) PubChem (129009945) PubChem (131841783) PubChem (132275078) PubChem (118213779) PubChem (118705495) PubChem (122691713) PubChem (124226132) PubChem (124226133) PubChem (124226134) PubChem (124464538) PubChem (12313981) PubChem (124761786) PubChem (124761787) PubChem (124761788) PubChem (124761789) PubChem (125040358) PubChem (125040360) PubChem (125121198) PubChem (129014632) PubChem (129014634) PubChem (129014635) PubChem (129313238) PubChem (152952600) PubChem (134771120) PubChem (162873319) PubChem (137404838) PubChem (161153506) PubChem (163199098) PubChem (164850471) PubChem (172091638) PubChem (173719997) | |||
| 59 | DIA, QI (32, 3E) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 2 | Chemie (SF4) | |||
| 60 | GIA, UI, XDA, XZA (5A, 5I, G8, C5) | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) | |||
| 61 | AIA, EZA, FZA (1G, 14) | THERMINE | non-polymer | 188.3 | 3 | Chemie (SPE) PubChem (78350) | |||
| 62 | AAB, ABB, ACB, BAB, BBB... (13, J8, C5, 4E, L8...) | water | water | 18.0 | 3467 | Chemie (HOH) |
Sequence modifications
13, 1G: 0 - 1541 (GenBank: 55771382)
1H, 14: 1 - 2907 (GenBank: 55771382)
| PDB | External Database | Details |
|---|---|---|
| G 1542 | - | expression tag |
| C 1543 | - | expression tag |
| U 1544 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| U 161 | Unk 9395 | conflict |
| A 654 | G 9920 | conflict |
| C 654 | G 9924 | conflict |
| G 654 | C 9935 | conflict |
| A 654 | C 9939 | conflict |
| U 1059 | G 10344 | conflict |
| A 1080 | C 10366 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 109 |
| Total formula weight | 4507172.6 | |
| Non-Polymers* | Number of molecules | 1269 |
| Total formula weight | 33336.8 | |
| All* | Total formula weight | 4540509.4 |
