6SKG
Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain
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 (Aa) | 16S ribosomal RNA | polymer | 1498 | 487394.9 | 1 | Thermococcus kodakarensis | ||
| 2 | B (Ab) | 30S ribosomal protein S2 | polymer | 201 | 23039.8 | 1 | UniProt (Q5JJD2) Pfam (PF00318) | Thermococcus kodakarensis | |
| 3 | C (Ac) | 30S ribosomal protein S3 | polymer | 209 | 23390.2 | 1 | UniProt (Q5JDH5) Pfam (PF07650) Pfam (PF00189) | Thermococcus kodakarensis | |
| 4 | D (Ad) | 30S ribosomal protein S3Ae | polymer | 200 | 23064.9 | 1 | UniProt (Q5JGM4) Pfam (PF01015) | Thermococcus kodakarensis | Ribosomal protein S1e |
| 5 | E (Ae) | 30S ribosomal protein S4 | polymer | 180 | 21240.6 | 1 | UniProt (Q5JJF2) Pfam (PF00163) Pfam (PF01479) | Thermococcus kodakarensis | |
| 6 | F (Af) | 30S ribosomal protein S4e | polymer | 243 | 27820.6 | 1 | UniProt (Q5JJG0) Pfam (PF00900) Pfam (PF08071) Pfam (PF01479) | Thermococcus kodakarensis | |
| 7 | G (Ag) | 30S ribosomal protein S5 | polymer | 235 | 26372.6 | 1 | UniProt (Q5JJG8) Pfam (PF00333) Pfam (PF03719) | Thermococcus kodakarensis | |
| 8 | H (Ah) | 30S ribosomal protein S6e | polymer | 125 | 13761.0 | 1 | UniProt (Q5JDK8) Pfam (PF01092) | Thermococcus kodakarensis | |
| 9 | I (Ai) | 30S ribosomal protein S7 | polymer | 215 | 24573.7 | 1 | UniProt (Q5JE04) Pfam (PF00177) | Thermococcus kodakarensis | |
| 10 | J (Aj) | 30S ribosomal protein S8 | polymer | 130 | 14602.1 | 1 | UniProt (Q5JJG3) Pfam (PF00410) | Thermococcus kodakarensis | |
| 11 | K (Ak) | 30S ribosomal protein S8e | polymer | 130 | 14548.0 | 1 | UniProt (Q5JGF3) Pfam (PF01201) | Thermococcus kodakarensis | |
| 12 | L (Al) | 30S ribosomal protein S9 | polymer | 135 | 15358.9 | 1 | UniProt (Q5JJE2) Pfam (PF00380) | Thermococcus kodakarensis | |
| 13 | M (Am) | 30S ribosomal protein S10 | polymer | 102 | 11716.7 | 1 | UniProt (Q5JFZ5) Pfam (PF00338) | Thermococcus kodakarensis | |
| 14 | N (An) | 30S ribosomal protein S11 | polymer | 140 | 15111.2 | 1 | UniProt (Q5JJF3) Pfam (PF00411) | Thermococcus kodakarensis | |
| 15 | O (Ao) | 30S ribosomal protein S12 | polymer | 147 | 16488.5 | 1 | UniProt (Q5JE20) Pfam (PF00164) | Thermococcus kodakarensis | |
| 16 | P (Ap) | 30S ribosomal protein S13 | polymer | 149 | 17025.9 | 1 | UniProt (Q5JJF1) Pfam (PF00416) | Thermococcus kodakarensis | |
| 17 | Q (Aq) | 30S ribosomal protein S15 | polymer | 151 | 17583.8 | 1 | UniProt (Q5JGJ4) Pfam (PF08069) Pfam (PF00312) | Thermococcus kodakarensis | |
| 18 | R (Ar) | 30S ribosomal protein S14 type Z | polymer | 56 | 6634.1 | 1 | UniProt (Q5JJG2) Pfam (PF00253) | Thermococcus kodakarensis | |
| 19 | S (As) | 30S ribosomal protein S17 | polymer | 114 | 13219.4 | 1 | UniProt (Q5JDH9) Pfam (PF00366) | Thermococcus kodakarensis | |
| 20 | MB, T (At, Bm) | 30S ribosomal protein S17e | polymer | 67 | 8036.4 | 2 | UniProt (Q5JDC7) Pfam (PF00833) | Thermococcus kodakarensis | |
| 21 | U (Au) | 30S ribosomal protein S19 | polymer | 133 | 15453.4 | 1 | UniProt (Q5JDH3) Pfam (PF00203) | Thermococcus kodakarensis | |
| 22 | V (Av) | 30S ribosomal protein S19e | polymer | 150 | 17304.0 | 1 | UniProt (Q5JGN5) Pfam (PF01090) | Thermococcus kodakarensis | |
| 23 | NB, W (Aw, Bn) | 30S ribosomal protein S24e | polymer | 98 | 11458.1 | 2 | UniProt (Q5JIY8) Pfam (PF01282) | Thermococcus kodakarensis | |
| 24 | X (Ax) | 30S ribosomal protein S27e | polymer | 65 | 7085.5 | 1 | UniProt (Q5JE50) Pfam (PF01667) | Thermococcus kodakarensis | |
| 25 | Y (Ay) | 30S ribosomal protein S28e | polymer | 70 | 7971.2 | 1 | UniProt (Q5JGR4) Pfam (PF01200) | Thermococcus kodakarensis | |
| 26 | Z (Az) | Predicted zinc-ribbon RNA-binding protein involved in translation | polymer | 62 | 7001.2 | 1 | UniProt (Q5JFE2) Pfam (PF07754) | Thermococcus kodakarensis | |
| 27 | AA (BA) | 23S ribosomal RNA | polymer | 3037 | 987981.4 | 1 | Thermococcus kodakarensis | ||
| 28 | BA (BB) | 5S ribosomal RNA | polymer | 126 | 40744.3 | 1 | GenBank (57158259) | Thermococcus kodakarensis | |
| 29 | CA (BC) | 50S ribosomal protein L2 | polymer | 239 | 26092.4 | 1 | UniProt (Q5JDH2) Pfam (PF00181) Pfam (PF03947) | Thermococcus kodakarensis | |
| 30 | DA (BD) | 50S ribosomal protein L3 | polymer | 346 | 39118.6 | 1 | UniProt (Q5JDJ0) Pfam (PF00297) | Thermococcus kodakarensis | |
| 31 | EA (BE) | 50S ribosomal protein L4 | polymer | 255 | 28768.6 | 1 | UniProt (Q5JDI0) Pfam (PF00573) | Thermococcus kodakarensis | |
| 32 | FA (BF) | 50S ribosomal protein L5 | polymer | 183 | 21027.6 | 1 | UniProt (Q5JJG1) Pfam (PF00281) Pfam (PF00673) | Thermococcus kodakarensis | |
| 33 | GA (BG) | 50S ribosomal protein L6 | polymer | 184 | 20888.3 | 1 | UniProt (Q5JJG4) Pfam (PF00347) | Thermococcus kodakarensis | |
| 34 | HA, IA (BH, BI) | 50S ribosomal protein L7Ae | polymer | 123 | 13454.6 | 2 | UniProt (Q5JGR3) Pfam (PF01248) | Thermococcus kodakarensis | Ribosomal protein L8e |
| 35 | JA (BJ) | 50S ribosomal protein L10e | polymer | 182 | 21116.6 | 1 | UniProt (Q5JDI6) Pfam (PF00252) | Thermococcus kodakarensis | |
| 36 | KA (BK) | 50S ribosomal protein L13 | polymer | 142 | 16316.2 | 1 | UniProt (Q5JJF6) Pfam (PF00572) | Thermococcus kodakarensis | |
| 37 | LA (BL) | 50S ribosomal protein L14 | polymer | 141 | 15181.9 | 1 | UniProt (Q5JJF8) Pfam (PF00238) | Thermococcus kodakarensis | |
| 38 | MA, NA (BM, BN) | 50S ribosomal protein L14e | polymer | 83 | 8968.5 | 2 | UniProt (Q5JJE4) | Thermococcus kodakarensis | |
| 39 | OA (BO) | 50S ribosomal protein L15 | polymer | 148 | 16571.4 | 1 | UniProt (Q5JJH0) Pfam (PF00828) | Thermococcus kodakarensis | |
| 40 | PA (BP) | 50S ribosomal protein L15e | polymer | 194 | 22607.9 | 1 | UniProt (Q5JH43) Pfam (PF00827) | Thermococcus kodakarensis | |
| 41 | QA (BQ) | 50S ribosomal protein L18 | polymer | 201 | 22895.4 | 1 | UniProt (Q5JJG7) Pfam (PF17144) | Thermococcus kodakarensis | |
| 42 | RA (BR) | 50S ribosomal protein L18e | polymer | 121 | 13799.2 | 1 | UniProt (Q5JJF5) Pfam (PF17135) | Thermococcus kodakarensis | |
| 43 | SA (BS) | 50S ribosomal protein L19e | polymer | 150 | 17667.2 | 1 | UniProt (Q5JJG6) Pfam (PF01280) Pfam (PF25476) | Thermococcus kodakarensis | |
| 44 | TA (BT) | 50S ribosomal protein L18Ae | polymer | 77 | 9227.7 | 1 | UniProt (Q5JGT3) Pfam (PF01775) | Thermococcus kodakarensis | 50S ribosomal protein L20e,50S ribosomal protein LX |
| 45 | UA (BU) | 50S ribosomal protein L21e | polymer | 98 | 11290.3 | 1 | UniProt (Q5JI51) Pfam (PF01157) | Thermococcus kodakarensis | |
| 46 | VA (BV) | 50S ribosomal protein L22 | polymer | 156 | 17838.8 | 1 | UniProt (Q5JDH4) Pfam (PF00237) | Thermococcus kodakarensis | |
| 47 | WA (BW) | 50S ribosomal protein L23 | polymer | 86 | 9915.8 | 1 | UniProt (Q5JDH1) Pfam (PF00276) | Thermococcus kodakarensis | |
| 48 | XA (BX) | 50S ribosomal protein L24 | polymer | 121 | 14225.8 | 1 | UniProt (Q5JJF9) Pfam (PF16906) Pfam (PF00467) | Thermococcus kodakarensis | |
| 49 | YA (BY) | 50S ribosomal protein L24e | polymer | 67 | 8111.6 | 1 | UniProt (Q5JGR5) Pfam (PF01246) | Thermococcus kodakarensis | |
| 50 | ZA (BZ) | 50S ribosomal protein L29 | polymer | 66 | 7937.5 | 1 | UniProt (Q5JDH6) Pfam (PF00831) | Thermococcus kodakarensis | |
| 51 | AB (Ba) | 50S ribosomal protein L30 | polymer | 155 | 17856.2 | 1 | UniProt (Q5JJG9) Pfam (PF00327) | Thermococcus kodakarensis | |
| 52 | BB (Bb) | 50S ribosomal protein L30e | polymer | 102 | 10972.8 | 1 | UniProt (Q5JE35) Pfam (PF01248) | Thermococcus kodakarensis | |
| 53 | CB (Bc) | 50S ribosomal protein L31e | polymer | 90 | 10354.3 | 1 | UniProt (Q5JGT5) Pfam (PF01198) | Thermococcus kodakarensis | |
| 54 | DB (Bd) | 50S ribosomal protein L32e | polymer | 125 | 14654.5 | 1 | UniProt (Q5JJG5) Pfam (PF01655) | Thermococcus kodakarensis | |
| 55 | EB (Be) | 50S ribosomal protein L34e | polymer | 90 | 10558.8 | 1 | UniProt (Q5JJF7) Pfam (PF01199) | Thermococcus kodakarensis | |
| 56 | FB (Bf) | Ribosomal protein eL35A | polymer | 101 | 11064.9 | 1 | Thermococcus kodakarensis | ||
| 57 | GB (Bg) | 50S ribosomal protein L37Ae | polymer | 86 | 9240.0 | 1 | UniProt (Q5JDM6) Pfam (PF01780) | Thermococcus kodakarensis | Ribosomal protein L43e |
| 58 | HB (Bh) | 50S ribosomal protein L37e | polymer | 63 | 7470.9 | 1 | UniProt (Q5JIE1) Pfam (PF01907) | Thermococcus kodakarensis | |
| 59 | IB (Bi) | 50S ribosomal protein L39e | polymer | 51 | 6262.7 | 1 | UniProt (Q5JGT6) Pfam (PF00832) | Thermococcus kodakarensis | |
| 60 | JB (Bj) | 50S ribosomal protein L40e | polymer | 51 | 5782.0 | 1 | UniProt (Q5JJD3) | Thermococcus kodakarensis | |
| 61 | KB (Bk) | LSU ribosomal protein L41E | polymer | 37 | 5051.4 | 1 | UniProt (Q5JEV0) | Thermococcus kodakarensis | |
| 62 | LB (Bl) | 50S ribosomal protein L44e | polymer | 94 | 11204.4 | 1 | UniProt (Q5JE51) Pfam (PF00935) | Thermococcus kodakarensis | |
| 63 | OB (Bo) | Nucleic acid-binding protein, containing C2H2 zinc-finger | polymer | 47 | 5485.6 | 1 | UniProt (Q5JFH3) Pfam (PF00096) | Thermococcus kodakarensis | |
| 64 | PB (Bp) | Predicted exosome subunit, UPF0023 family | polymer | 236 | 26873.1 | 1 | UniProt (Q5JIV0) Pfam (PF01172) Pfam (PF09377) Pfam (PF20268) | Thermococcus kodakarensis | |
| 65 | QB (Bq) | Unknown ribosomal protein | polymer | 34 | 2434.7 | 1 | Thermococcus kodakarensis | ||
| 66 | AC, BC, CC, DC, EC... (Bg, Bh, Bj, Bl, Bo...) | ZINC ION | non-polymer | 65.4 | 14 | Chemie (ZN) | |||
| 67 | AD, AE, BD, BE, CD... (BE, Bf, BF, Bg, BG...) | water | water | 18.0 | 3556 | Chemie (HOH) |
Sequence modifications
Ax: 1 - 65 (UniProt: Q5JE50)
| PDB | External Database | Details |
|---|---|---|
| Glu 64 | Leu 64 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 69 |
| Total formula weight | 2496188.5 | |
| Non-Polymers* | Number of molecules | 14 |
| Total formula weight | 915.7 | |
| All* | Total formula weight | 2497104.2 |
