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) | 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) | 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) | 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) Pfam (PF00687) | 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) | 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) | |||
| 58 | PI, ZHA (13, 1G) | PAROMOMYCIN | non-polymer | 615.6 | 2 | Chemie (PAR) | |||
| 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) | |||
| 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 |
