1YIT
Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (0) | 23S RIBOSOMAL RNA | polymer | 2922 | 946157.4 | 1 | GenBank (55229667) | HALOARCULA MARISMORTUI | |
| 2 | B (1) | 50S RIBOSOMAL PROTEIN L37E | polymer | 57 | 6330.2 | 1 | UniProt (P32410) Pfam (PF01907) | HALOARCULA MARISMORTUI | |
| 3 | C (2) | 50S RIBOSOMAL PROTEIN L39E | polymer | 50 | 6133.1 | 1 | UniProt (P22452) Pfam (PF00832) | HALOARCULA MARISMORTUI | |
| 4 | D (3) | 50S RIBOSOMAL PROTEIN L44E | polymer | 92 | 10815.2 | 1 | UniProt (P32411) Pfam (PF00935) | HALOARCULA MARISMORTUI | |
| 5 | E (8) | VIRGINIAMYCIN S1 | polymer | 7 | 841.9 | 1 | NOR (NOR00679) BIRD (PRD_000227) | STREPTOMYCES VIRGINIAE | VIRGINIAMYCIN FACTOR S1, VIRGINIAMYCIN S |
| 6 | F (9) | 5S RIBOSOMAL RNA | polymer | 122 | 39303.4 | 1 | GenBank (3377778) | HALOARCULA MARISMORTUI | |
| 7 | G (A) | 50S RIBOSOMAL PROTEIN L2P | polymer | 240 | 25354.7 | 1 | UniProt (P20276) Pfam (PF00181) Pfam (PF03947) | HALOARCULA MARISMORTUI | |
| 8 | H (B) | 50S RIBOSOMAL PROTEIN L3P | polymer | 338 | 37396.4 | 1 | GenBank (55378384) Pfam (PF00297) UniProt (by SIFTS) (P20279) | HALOARCULA MARISMORTUI | |
| 9 | I (C) | 50S RIBOSOMAL PROTEIN L4E | polymer | 246 | 26442.1 | 1 | UniProt (P12735) Pfam (PF00573) | HALOARCULA MARISMORTUI | |
| 10 | J (D) | 50S RIBOSOMAL PROTEIN L5P | polymer | 177 | 19551.7 | 1 | UniProt (P14124) Pfam (PF00281) Pfam (PF00673) | HALOARCULA MARISMORTUI | |
| 11 | K (E) | 50S RIBOSOMAL PROTEIN L6P | polymer | 178 | 19961.7 | 1 | UniProt (P14135) Pfam (PF00347) | HALOARCULA MARISMORTUI | |
| 12 | L (F) | 50S RIBOSOMAL PROTEIN L7AE | polymer | 120 | 12791.9 | 1 | UniProt (P12743) Pfam (PF01248) | HALOARCULA MARISMORTUI | |
| 13 | M (G) | ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG | polymer | 348 | 37213.8 | 1 | UniProt (P15825) Pfam (PF00466) Pfam (PF17777) | HALOARCULA MARISMORTUI | |
| 14 | N (H) | 50S RIBOSOMAL PROTEIN L10E | polymer | 177 | 19942.7 | 1 | GenBank (55231756) Pfam (PF00252) UniProt (by SIFTS) (P60617) | HALOARCULA MARISMORTUI | |
| 15 | O (I) | 50S RIBOSOMAL PROTEIN L11P | polymer | 162 | 17097.5 | 1 | GenBank (132647) Pfam (PF03946) Pfam (PF00298) UniProt (by SIFTS) (P14122) | HALOARCULA MARISMORTUI | |
| 16 | P (J) | 50S RIBOSOMAL PROTEIN L13P | polymer | 145 | 16249.2 | 1 | UniProt (P29198) Pfam (PF00572) | HALOARCULA MARISMORTUI | |
| 17 | Q (K) | 50S RIBOSOMAL PROTEIN L14P | polymer | 132 | 14191.2 | 1 | UniProt (P22450) Pfam (PF00238) | HALOARCULA MARISMORTUI | |
| 18 | R (L) | 50S RIBOSOMAL PROTEIN L15P | polymer | 165 | 18005.4 | 1 | UniProt (P12737) Pfam (PF00828) | HALOARCULA MARISMORTUI | |
| 19 | S (M) | 50S RIBOSOMAL PROTEIN L15E | polymer | 195 | 22275.1 | 1 | GenBank (55231501) Pfam (PF00827) UniProt (by SIFTS) (P60618) | HALOARCULA MARISMORTUI | |
| 20 | T (N) | 50S RIBOSOMAL PROTEIN L18P | polymer | 187 | 20640.9 | 1 | UniProt (P14123) Pfam (PF17144) | HALOARCULA MARISMORTUI | |
| 21 | U (O) | 50S RIBOSOMAL PROTEIN L18E | polymer | 116 | 12438.9 | 1 | UniProt (P12733) Pfam (PF00828) | HALOARCULA MARISMORTUI | |
| 22 | V (P) | 50S RIBOSOMAL PROTEIN L19E | polymer | 149 | 16796.5 | 1 | UniProt (P14119) Pfam (PF01280) | HALOARCULA MARISMORTUI | |
| 23 | W (Q) | 50S RIBOSOMAL PROTEIN L21E | polymer | 96 | 10567.8 | 1 | UniProt (P12734) Pfam (PF01157) | HALOARCULA MARISMORTUI | |
| 24 | X (R) | 50S RIBOSOMAL PROTEIN L22P | polymer | 155 | 16966.9 | 1 | UniProt (P10970) Pfam (PF00237) | HALOARCULA MARISMORTUI | |
| 25 | Y (S) | 50S RIBOSOMAL PROTEIN L23P | polymer | 85 | 9612.5 | 1 | UniProt (P12732) Pfam (PF00276) | HALOARCULA MARISMORTUI | |
| 26 | Z (T) | 50S RIBOSOMAL PROTEIN L24P | polymer | 120 | 13671.0 | 1 | UniProt (P10972) Pfam (PF16906) Pfam (PF00467) | HALOARCULA MARISMORTUI | |
| 27 | AA (U) | 50S RIBOSOMAL PROTEIN L24E | polymer | 66 | 7233.7 | 1 | UniProt (P14116) Pfam (PF01246) | HALOARCULA MARISMORTUI | |
| 28 | BA (V) | 50S RIBOSOMAL PROTEIN L29P | polymer | 71 | 7889.9 | 1 | UniProt (P10971) Pfam (PF00831) | HALOARCULA MARISMORTUI | |
| 29 | CA (W) | 50S RIBOSOMAL PROTEIN L30P | polymer | 154 | 17062.9 | 1 | UniProt (P14121) Pfam (PF00327) | HALOARCULA MARISMORTUI | |
| 30 | DA (X) | 50S RIBOSOMAL PROTEIN L31E | polymer | 92 | 10384.6 | 1 | UniProt (P18138) Pfam (PF01198) | HALOARCULA MARISMORTUI | |
| 31 | EA (Y) | 50S RIBOSOMAL PROTEIN L32E | polymer | 241 | 26455.7 | 1 | UniProt (P12736) Pfam (PF14520) Pfam (PF01655) | HALOARCULA MARISMORTUI | |
| 32 | FA (Z) | 50S RIBOSOMAL PROTEIN L37AE | polymer | 83 | 9409.3 | 1 | GenBank (55231162) Pfam (PF01780) UniProt (by SIFTS) (P60619) | HALOARCULA MARISMORTUI | |
| 33 | AB, AC, AD, AE, AI... (0, A, Y, B, K...) | MAGNESIUM ION | non-polymer | 24.3 | 118 | Chemie (MG) | |||
| 34 | LE (0) | POTASSIUM ION | non-polymer | 39.1 | 1 | Chemie (K) | |||
| 35 | AF, AG, AH, BF, BG... (0, A, C, H, J...) | SODIUM ION | non-polymer | 23.0 | 85 | Chemie (NA) | |||
| 36 | CI, CJ, FI, HH, IH... (A, Y, B, 0, J...) | CHLORIDE ION | non-polymer | 35.5 | 22 | Chemie (CL) | |||
| 37 | RH (0) | VIRGINIAMYCIN M1 | non-polymer | 525.6 | 1 | Chemie (VIR) | |||
| 38 | AJ, DJ, SH, SI, VH (U, Z, 1, O, 3) | CADMIUM ION | non-polymer | 112.4 | 5 | Chemie (CD) |
Sequence modifications
0: 1 - 2922 (GenBank: 55229667)
K: 1 - 132 (UniProt: P22450)
M: 0 - 194 (GenBank: 55231501)
Z: 10 - 92 (GenBank: 55231162)
| PDB | External Database | Details |
|---|---|---|
| 1ma 628 | A 627 | modified residue |
| Omu 2587 | U 2586 | modified residue |
| Omg 2588 | G 2587 | modified residue |
| Ur3 2619 | U 2618 | modified residue |
| Psu 2621 | U 2620 | modified residue |
| PDB | External Database | Details |
|---|---|---|
| Leu 44 | His 44 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Glu 13 | Lys 14 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 10 | Ser 34 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 32 |
| Total formula weight | 1475185.5 | |
| Non-Polymers* | Number of molecules | 232 |
| Total formula weight | 6728.9 | |
| All* | Total formula weight | 1481914.3 |
