1N8R
Structure of large ribosomal subunit in complex with virginiamycin M
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | 23S ribosomal RNA | polymer | 2922 | 946034.4 | 1 | GenBank (3377779) | Haloarcula marismortui | |
| 2 | B (B) | 5S ribosomal RNA | polymer | 122 | 39318.4 | 1 | GenBank (3377779) | Haloarcula marismortui | |
| 3 | C (C) | 50S ribosomal protein L2P | polymer | 239 | 25237.5 | 1 | UniProt (P20276) Pfam (PF00181) Pfam (PF03947) | Haloarcula marismortui | Hmal2, HL4 |
| 4 | D (D) | 50S ribosomal protein L3P | polymer | 337 | 37265.2 | 1 | UniProt (P20279) Pfam (PF00297) | Haloarcula marismortui | Hmal3, HL1 |
| 5 | E (E) | 50S ribosomal protein L4E | polymer | 246 | 26442.1 | 1 | UniProt (P12735) Pfam (PF00573) | Haloarcula marismortui | Hmal4, HL6 |
| 6 | F (F) | 50S ribosomal protein L5P | polymer | 176 | 19420.5 | 1 | UniProt (P14124) Pfam (PF00673) Pfam (PF00281) | Haloarcula marismortui | Hmal5, HL13 |
| 7 | G (G) | 50S ribosomal protein L6P | polymer | 177 | 19830.5 | 1 | UniProt (P14135) Pfam (PF00347) | Haloarcula marismortui | Hmal6, HL10 |
| 8 | H (H) | 50S ribosomal protein L7Ae | polymer | 119 | 12600.8 | 1 | UniProt (P12743) Pfam (PF01248) | Haloarcula marismortui | HS6 |
| 9 | I (I) | Acidic ribosomal protein P0 homolog | polymer | 348 | 37213.8 | 1 | UniProt (P15825) Pfam (PF00466) Pfam (PF17777) | Haloarcula marismortui | L10E, HMaL10 |
| 10 | J (J) | 50S ribosomal protein L10e | polymer | 167 | 18022.5 | 1 | Pfam (PF00252) UniProt (by SIFTS) (P60617) | Haloarcula marismortui | |
| 11 | K (K) | 50S ribosomal protein L13P | polymer | 145 | 16249.2 | 1 | UniProt (P29198) Pfam (PF00572) | Haloarcula marismortui | Hmal13 |
| 12 | L (L) | 50S ribosomal protein L14P | polymer | 132 | 14216.2 | 1 | UniProt (P22450) Pfam (PF00238) | Haloarcula marismortui | Hmal14, HL27 |
| 13 | M (M) | 50S ribosomal protein L15P | polymer | 164 | 17874.2 | 1 | UniProt (P12737) Pfam (PF00828) | Haloarcula marismortui | Hmal15, HL9 |
| 14 | N (N) | 50S ribosomal protein L15E | polymer | 194 | 22856.6 | 1 | Pfam (PF00827) UniProt (by SIFTS) (P60618) | Haloarcula marismortui | |
| 15 | O (O) | 50S ribosomal protein L18P | polymer | 186 | 20509.7 | 1 | UniProt (P14123) Pfam (PF17144) | Haloarcula marismortui | Hmal18, HL12 |
| 16 | P (P) | 50S ribosomal protein L18E | polymer | 115 | 12307.7 | 1 | UniProt (P12733) Pfam (PF00828) | Haloarcula marismortui | HL29, L19 |
| 17 | Q (Q) | 50S ribosomal protein L19E | polymer | 148 | 16631.3 | 1 | UniProt (P14119) Pfam (PF01280) | Haloarcula marismortui | Hmal19, HL24 |
| 18 | R (R) | 50S ribosomal protein L21e | polymer | 95 | 10436.6 | 1 | UniProt (P12734) Pfam (PF01157) | Haloarcula marismortui | HL31 |
| 19 | S (S) | 50S ribosomal protein L22P | polymer | 154 | 16835.7 | 1 | UniProt (P10970) Pfam (PF00237) | Haloarcula marismortui | Hmal22, HL23 |
| 20 | T (T) | 50S ribosomal protein L23P | polymer | 84 | 9481.3 | 1 | UniProt (P12732) Pfam (PF00276) | Haloarcula marismortui | Hmal23, HL25, L21 |
| 21 | U (U) | 50S ribosomal protein L24P | polymer | 119 | 13539.8 | 1 | UniProt (P10972) Pfam (PF16906) Pfam (PF00467) | Haloarcula marismortui | Hmal24, HL16, HL15 |
| 22 | V (V) | 50S ribosomal protein L24E | polymer | 66 | 7233.7 | 1 | UniProt (P14116) Pfam (PF01246) | Haloarcula marismortui | HL21/HL22 |
| 23 | W (W) | 50S ribosomal protein L29P | polymer | 70 | 7758.7 | 1 | UniProt (P10971) Pfam (PF00831) | Haloarcula marismortui | Hmal29, HL33 |
| 24 | X (X) | 50S ribosomal protein L30P | polymer | 154 | 17062.9 | 1 | UniProt (P14121) Pfam (PF00327) | Haloarcula marismortui | Hmal30, HL20, HL16 |
| 25 | Y (Y) | 50S ribosomal protein L31E | polymer | 91 | 10253.4 | 1 | UniProt (P18138) Pfam (PF01198) | Haloarcula marismortui | L34, HL30 |
| 26 | Z (Z) | 50S ribosomal protein L32E | polymer | 240 | 26324.5 | 1 | UniProt (P12736) Pfam (PF14520) Pfam (PF01655) | Haloarcula marismortui | HL5 |
| 27 | AA (1) | 50S ribosomal protein L37AE | polymer | 73 | 8097.8 | 1 | Pfam (PF01780) UniProt (by SIFTS) (P60619) | Haloarcula marismortui | |
| 28 | BA (2) | 50S ribosomal protein L37e | polymer | 56 | 6199.0 | 1 | UniProt (P32410) Pfam (PF01907) | Haloarcula marismortui | L35e |
| 29 | CA (3) | 50S ribosomal protein L39e | polymer | 48 | 5844.7 | 1 | UniProt (P22452) Pfam (PF00832) | Haloarcula marismortui | HL39e, HL46e |
| 30 | DA (4) | 50S ribosomal protein L44E | polymer | 92 | 10815.2 | 1 | UniProt (P32411) Pfam (PF00935) | Haloarcula marismortui | LA, HLA |
| 31 | EA (A) | VIRGINIAMYCIN M1 | non-polymer | 525.6 | 1 | Chemie (VIR) | |||
| 32 | AB, AC, AD, AE, BB... (A, L, B, C, U...) | MAGNESIUM ION | non-polymer | 24.3 | 117 | Chemie (MG) | |||
| 33 | KE (A) | POTASSIUM ION | non-polymer | 39.1 | 1 | Chemie (K) | |||
| 34 | AF, AG, AH, BF, BG... (A, M, N, R, S...) | SODIUM ION | non-polymer | 23.0 | 86 | Chemie (NA) | |||
| 35 | AI, BI, BJ, DI, EH... (K, 4, L, A, M...) | CHLORIDE ION | non-polymer | 35.5 | 22 | Chemie (CL) | |||
| 36 | AJ, JI, SI, WI, XI (4, P, V, 1, 2) | CADMIUM ION | non-polymer | 112.4 | 5 | Chemie (CD) | |||
| 37 | AK, BK, CJ, CK, DJ... (Y, Z, A, 1, B...) | water | water | 18.0 | 7882 | Chemie (HOH) |
Sequence modifications
D: 1 - 337 (UniProt: P20279)
| PDB | External Database | Details |
|---|---|---|
| - | Pro 310 | deletion |
| Arg 310 | Phe 311 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 30 |
| Total formula weight | 1451914.1 | |
| Non-Polymers* | Number of molecules | 232 |
| Total formula weight | 6727.5 | |
| All* | Total formula weight | 1458641.7 |
