4B3M
Crystal structure of the 30S ribosome in complex with compound 1
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | 16S RIBOSOMAL RNA | polymer | 1521 | 493652.2 | 1 | GenBank (55771382) | THERMUS THERMOPHILUS HB8 | |
| 2 | B (B) | 30S RIBOSOMAL PROTEIN S2 | polymer | 256 | 29317.7 | 1 | UniProt (P80371) Pfam (PF00318) | THERMUS THERMOPHILUS HB8 | |
| 3 | C (C) | 30S RIBOSOMAL PROTEIN S3 | polymer | 239 | 26751.1 | 1 | UniProt (P80372) Pfam (PF07650) Pfam (PF00189) | THERMUS THERMOPHILUS HB8 | |
| 4 | D (D) | 30S RIBOSOMAL PROTEIN S4 | polymer | 208 | 24242.3 | 1 | UniProt (P80373) Pfam (PF00163) Pfam (PF01479) | THERMUS THERMOPHILUS HB8 | |
| 5 | E (E) | 30S RIBOSOMAL PROTEIN S5 | polymer | 161 | 17452.2 | 1 | UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) | THERMUS THERMOPHILUS HB8 | |
| 6 | F (F) | 30S RIBOSOMAL PROTEIN S6 | polymer | 101 | 11988.8 | 1 | UniProt (Q5SLP8) Pfam (PF01250) | THERMUS THERMOPHILUS HB8 | TS9 |
| 7 | G (G) | 30S RIBOSOMAL PROTEIN S7 | polymer | 155 | 17919.8 | 1 | UniProt (P17291) Pfam (PF00177) | THERMUS THERMOPHILUS HB8 | |
| 8 | H (H) | 30S RIBOSOMAL PROTEIN S8 | polymer | 138 | 15868.6 | 1 | UniProt (Q5SHQ2) Pfam (PF00410) UniProt (by SIFTS) (P0DOY9) | THERMUS THERMOPHILUS HB8 | |
| 9 | I (I) | 30S RIBOSOMAL PROTEIN S9 | polymer | 128 | 14429.7 | 1 | UniProt (P80374) Pfam (PF00380) | THERMUS THERMOPHILUS HB8 | |
| 10 | J (J) | 30S RIBOSOMAL PROTEIN S10 | polymer | 104 | 11823.8 | 1 | UniProt (Q5SHN7) Pfam (PF00338) | THERMUS THERMOPHILUS HB8 | |
| 11 | K (K) | 30S RIBOSOMAL PROTEIN S11 | polymer | 129 | 13737.9 | 1 | UniProt (P80376) Pfam (PF00411) | THERMUS THERMOPHILUS HB8 | |
| 12 | L (L) | 30S RIBOSOMAL PROTEIN S12 | polymer | 132 | 14637.4 | 1 | UniProt (Q5SHN3) Pfam (PF00164) | THERMUS THERMOPHILUS HB8 | |
| 13 | M (M) | 30S RIBOSOMAL PROTEIN S13 | polymer | 126 | 14338.9 | 1 | UniProt (P80377) Pfam (PF00416) | THERMUS THERMOPHILUS HB8 | |
| 14 | N (N) | 30S RIBOSOMAL PROTEIN S14 TYPE Z | polymer | 60 | 7027.5 | 1 | UniProt (Q5SHQ1) Pfam (PF00253) UniProt (by SIFTS) (P0DOY6) | THERMUS THERMOPHILUS HB8 | |
| 15 | O (O) | 30S RIBOSOMAL PROTEIN S15 | polymer | 88 | 10447.2 | 1 | UniProt (Q5SJ76) Pfam (PF00312) | THERMUS THERMOPHILUS HB8 | |
| 16 | P (P) | 30S RIBOSOMAL PROTEIN S16 | polymer | 88 | 10410.0 | 1 | UniProt (Q5SJH3) Pfam (PF00886) | THERMUS THERMOPHILUS HB8 | |
| 17 | Q (Q) | 30S RIBOSOMAL PROTEIN S17 | polymer | 104 | 12193.5 | 1 | UniProt (Q5SHP7) Pfam (PF00366) UniProt (by SIFTS) (P0DOY7) | THERMUS THERMOPHILUS HB8 | |
| 18 | R (R) | 30S RIBOSOMAL PROTEIN S18 | polymer | 88 | 10244.3 | 1 | UniProt (Q5SLQ0) Pfam (PF01084) | THERMUS THERMOPHILUS HB8 | |
| 19 | S (S) | 30S RIBOSOMAL PROTEIN S19 | polymer | 92 | 10474.3 | 1 | UniProt (Q5SHP2) Pfam (PF00203) | THERMUS THERMOPHILUS HB8 | |
| 20 | T (T) | 30S RIBOSOMAL PROTEIN S20 | polymer | 106 | 11722.1 | 1 | UniProt (P80380) Pfam (PF01649) | THERMUS THERMOPHILUS HB8 | |
| 21 | U (V) | 30S RIBOSOMAL PROTEIN THX | polymer | 26 | 3218.8 | 1 | UniProt (Q5SIH3) Pfam (PF17070) | THERMUS THERMOPHILUS HB8 | |
| 22 | V (W) | 5'-R(*UP*UP*CP*AP*AP*AP)-3' | polymer | 6 | 1860.2 | 1 | THERMUS THERMOPHILUS HB8 | MRNA | |
| 23 | W (Z) | 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3' | polymer | 16 | 5161.1 | 1 | THERMUS THERMOPHILUS HB8 | ANTICODON STEM LOOP ASL | |
| 24 | AA, AB, AC, AD, AE... (A, B, D, E, H...) | MAGNESIUM ION | non-polymer | 24.3 | 240 | Chemie (MG) | |||
| 25 | CF, DF, DJ, EF, FF... (A) | POTASSIUM ION | non-polymer | 39.1 | 17 | Chemie (K) | |||
| 26 | PI (A) | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside | non-polymer | 703.7 | 1 | Chemie (ON0) | |||
| 27 | FJ, SJ (D, N) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 28 | XJ (A) | water | water | 18.0 | 7 | Chemie (HOH) |
Sequence modifications
I: 0 - 127 (UniProt: P80374)
Q: 1 - 104 (UniProt: Q5SHP7)
R: -14 - 73 (UniProt: Q5SLQ0)
T: -6 - 99 (UniProt: P80380)
| PDB | External Database | Details |
|---|---|---|
| Arg 57 | His 58 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gln 95 | Glu 96 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 45 | Ala 60 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Val 34 | Ile 41 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 23 |
| Total formula weight | 788919.1 | |
| Non-Polymers* | Number of molecules | 260 |
| Total formula weight | 7332.4 | |
| All* | Total formula weight | 796251.5 |
