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 | 0 | 23S RIBOSOMAL RNA | polymer | 2922 | 946157.4 | 1 | GenBank (55229667) | HALOARCULA MARISMORTUI | |
2 | 1 | 50S RIBOSOMAL PROTEIN L37E | polymer | 57 | 6330.2 | 1 | UniProt (P32410) Pfam (PF01907) In PDB | HALOARCULA MARISMORTUI | |
3 | 2 | 50S RIBOSOMAL PROTEIN L39E | polymer | 50 | 6133.1 | 1 | UniProt (P22452) Pfam (PF00832) In PDB | HALOARCULA MARISMORTUI | |
4 | 3 | 50S RIBOSOMAL PROTEIN L44E | polymer | 92 | 10815.2 | 1 | UniProt (P32411) Pfam (PF00935) In PDB | HALOARCULA MARISMORTUI | |
5 | 8 | VIRGINIAMYCIN S1 | polymer | 7 | 841.9 | 1 | NOR (NOR00679) BIRD (PRD_000227) | STREPTOMYCES VIRGINIAE | VIRGINIAMYCIN FACTOR S1, VIRGINIAMYCIN S |
6 | 9 | 5S RIBOSOMAL RNA | polymer | 122 | 39303.4 | 1 | GenBank (3377778) | HALOARCULA MARISMORTUI | |
7 | A | 50S RIBOSOMAL PROTEIN L2P | polymer | 240 | 25354.7 | 1 | UniProt (P20276) Pfam (PF00181) Pfam (PF03947) In PDB | HALOARCULA MARISMORTUI | |
8 | B | 50S RIBOSOMAL PROTEIN L3P | polymer | 338 | 37396.4 | 1 | GenBank (55378384) Pfam (PF00297) UniProt (by SIFTS) (P20279) In PDB | HALOARCULA MARISMORTUI | |
9 | C | 50S RIBOSOMAL PROTEIN L4E | polymer | 246 | 26442.1 | 1 | UniProt (P12735) Pfam (PF00573) In PDB | HALOARCULA MARISMORTUI | |
10 | D | 50S RIBOSOMAL PROTEIN L5P | polymer | 177 | 19551.7 | 1 | UniProt (P14124) Pfam (PF00281) Pfam (PF00673) In PDB | HALOARCULA MARISMORTUI | |
11 | E | 50S RIBOSOMAL PROTEIN L6P | polymer | 178 | 19961.7 | 1 | UniProt (P14135) Pfam (PF00347) In PDB | HALOARCULA MARISMORTUI | |
12 | F | 50S RIBOSOMAL PROTEIN L7AE | polymer | 120 | 12791.9 | 1 | UniProt (P12743) Pfam (PF01248) In PDB | HALOARCULA MARISMORTUI | |
13 | G | ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG | polymer | 348 | 37213.8 | 1 | UniProt (P15825) Pfam (PF00466) Pfam (PF17777) In PDB | HALOARCULA MARISMORTUI | |
14 | H | 50S RIBOSOMAL PROTEIN L10E | polymer | 177 | 19942.7 | 1 | GenBank (55231756) Pfam (PF00252) UniProt (by SIFTS) (P60617) In PDB | HALOARCULA MARISMORTUI | |
15 | I | 50S RIBOSOMAL PROTEIN L11P | polymer | 162 | 17097.5 | 1 | GenBank (132647) Pfam (PF03946) Pfam (PF00298) UniProt (by SIFTS) (P14122) In PDB | HALOARCULA MARISMORTUI | |
16 | J | 50S RIBOSOMAL PROTEIN L13P | polymer | 145 | 16249.2 | 1 | UniProt (P29198) Pfam (PF00572) In PDB | HALOARCULA MARISMORTUI | |
17 | K | 50S RIBOSOMAL PROTEIN L14P | polymer | 132 | 14191.2 | 1 | UniProt (P22450) Pfam (PF00238) In PDB | HALOARCULA MARISMORTUI | |
18 | L | 50S RIBOSOMAL PROTEIN L15P | polymer | 165 | 18005.4 | 1 | UniProt (P12737) Pfam (PF00828) In PDB | HALOARCULA MARISMORTUI | |
19 | M | 50S RIBOSOMAL PROTEIN L15E | polymer | 195 | 22275.1 | 1 | GenBank (55231501) Pfam (PF00827) UniProt (by SIFTS) (P60618) In PDB | HALOARCULA MARISMORTUI | |
20 | N | 50S RIBOSOMAL PROTEIN L18P | polymer | 187 | 20640.9 | 1 | UniProt (P14123) Pfam (PF17144) In PDB | HALOARCULA MARISMORTUI | |
21 | O | 50S RIBOSOMAL PROTEIN L18E | polymer | 116 | 12438.9 | 1 | UniProt (P12733) Pfam (PF00828) In PDB | HALOARCULA MARISMORTUI | |
22 | P | 50S RIBOSOMAL PROTEIN L19E | polymer | 149 | 16796.5 | 1 | UniProt (P14119) Pfam (PF01280) In PDB | HALOARCULA MARISMORTUI | |
23 | Q | 50S RIBOSOMAL PROTEIN L21E | polymer | 96 | 10567.8 | 1 | UniProt (P12734) Pfam (PF01157) In PDB | HALOARCULA MARISMORTUI | |
24 | R | 50S RIBOSOMAL PROTEIN L22P | polymer | 155 | 16966.9 | 1 | UniProt (P10970) Pfam (PF00237) In PDB | HALOARCULA MARISMORTUI | |
25 | S | 50S RIBOSOMAL PROTEIN L23P | polymer | 85 | 9612.5 | 1 | UniProt (P12732) Pfam (PF00276) In PDB | HALOARCULA MARISMORTUI | |
26 | T | 50S RIBOSOMAL PROTEIN L24P | polymer | 120 | 13671.0 | 1 | UniProt (P10972) Pfam (PF16906) Pfam (PF00467) In PDB | HALOARCULA MARISMORTUI | |
27 | U | 50S RIBOSOMAL PROTEIN L24E | polymer | 66 | 7233.7 | 1 | UniProt (P14116) Pfam (PF01246) In PDB | HALOARCULA MARISMORTUI | |
28 | V | 50S RIBOSOMAL PROTEIN L29P | polymer | 71 | 7889.9 | 1 | UniProt (P10971) Pfam (PF00831) In PDB | HALOARCULA MARISMORTUI | |
29 | W | 50S RIBOSOMAL PROTEIN L30P | polymer | 154 | 17062.9 | 1 | UniProt (P14121) Pfam (PF00327) In PDB | HALOARCULA MARISMORTUI | |
30 | X | 50S RIBOSOMAL PROTEIN L31E | polymer | 92 | 10384.6 | 1 | UniProt (P18138) Pfam (PF01198) In PDB | HALOARCULA MARISMORTUI | |
31 | Y | 50S RIBOSOMAL PROTEIN L32E | polymer | 241 | 26455.7 | 1 | UniProt (P12736) Pfam (PF14520) Pfam (PF01655) In PDB | HALOARCULA MARISMORTUI | |
32 | Z | 50S RIBOSOMAL PROTEIN L37AE | polymer | 83 | 9409.3 | 1 | GenBank (55231162) Pfam (PF01780) UniProt (by SIFTS) (P60619) In PDB | HALOARCULA MARISMORTUI | |
33 | 0, A, Y, B, K... | MAGNESIUM ION | non-polymer | 24.3 | 118 | Chemie (MG) | |||
34 | 0 | POTASSIUM ION | non-polymer | 39.1 | 1 | Chemie (K) | |||
35 | 0, A, C, H, J... | SODIUM ION | non-polymer | 23.0 | 85 | Chemie (NA) | |||
36 | A, Y, B, 0, J... | CHLORIDE ION | non-polymer | 35.5 | 22 | Chemie (CL) | |||
37 | 0 | VIRGINIAMYCIN M1 | non-polymer | 525.6 | 1 | Chemie (VIR) | |||
38 | 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 |