5DM7
Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (0) | 50S ribosomal protein L1 | polymer | 224 | 23514.9 | 1 | UniProt (Q9RSS8) Pfam (PF00687) | Deinococcus radiodurans | |
| 2 | B (A) | 50S ribosomal protein L2 | polymer | 274 | 29918.5 | 1 | UniProt (Q9RXJ9) Pfam (PF00181) Pfam (PF03947) | Deinococcus radiodurans | |
| 3 | C (B) | 50S ribosomal protein L3 | polymer | 205 | 21962.5 | 1 | UniProt (Q9RXK2) Pfam (PF00297) | Deinococcus radiodurans | |
| 4 | D (C) | 50S ribosomal protein L4 | polymer | 197 | 21405.2 | 1 | UniProt (Q9RXK1) Pfam (PF00573) | Deinococcus radiodurans | |
| 5 | E (D) | 50S ribosomal protein L5 | polymer | 177 | 19992.5 | 1 | UniProt (Q9RXJ0) Pfam (PF00673) Pfam (PF00281) | Deinococcus radiodurans | |
| 6 | F (E) | 50S ribosomal protein L6 | polymer | 171 | 18266.0 | 1 | UniProt (Q9RSL3) Pfam (PF00347) | Deinococcus radiodurans | |
| 7 | G (F) | 50S ribosomal protein L11 | polymer | 144 | 14945.2 | 1 | UniProt (Q9RSS7) Pfam (PF03946) Pfam (PF00298) | Deinococcus radiodurans | |
| 8 | H (G) | 50S ribosomal protein L13 | polymer | 142 | 15837.3 | 1 | UniProt (Q9RXY1) Pfam (PF00572) | Deinococcus radiodurans | |
| 9 | I (H) | 50S ribosomal protein L14 | polymer | 134 | 14256.5 | 1 | UniProt (Q9RXJ2) Pfam (PF00238) | Deinococcus radiodurans | |
| 10 | J (I) | 50S ribosomal protein L15 | polymer | 141 | 15177.3 | 1 | UniProt (Q9RSK9) Pfam (PF00828) | Deinococcus radiodurans | |
| 11 | K (J) | 50S ribosomal protein L16 | polymer | 136 | 15543.2 | 1 | UniProt (Q9RXJ5) Pfam (PF00252) | Deinococcus radiodurans | |
| 12 | L (K) | 50S ribosomal protein L17 | polymer | 113 | 12538.5 | 1 | UniProt (Q9RSJ5) Pfam (PF01196) | Deinococcus radiodurans | |
| 13 | M (L) | 50S ribosomal protein L18 | polymer | 104 | 11070.7 | 1 | UniProt (Q9RSL2) Pfam (PF00861) | Deinococcus radiodurans | |
| 14 | N (M) | 50S ribosomal protein L19 | polymer | 109 | 12290.0 | 1 | UniProt (Q9RWB4) Pfam (PF01245) | Deinococcus radiodurans | |
| 15 | O (N) | 50S ribosomal protein L20 | polymer | 117 | 13860.1 | 1 | UniProt (Q9RSW7) Pfam (PF00453) | Deinococcus radiodurans | |
| 16 | P (O) | 50S ribosomal protein L21 | polymer | 94 | 10518.0 | 1 | UniProt (Q9RY64) Pfam (PF00829) | Deinococcus radiodurans | |
| 17 | Q (P) | 50S ribosomal protein L22 | polymer | 127 | 14432.0 | 1 | UniProt (Q9RXJ7) Pfam (PF00237) | Deinococcus radiodurans | |
| 18 | R (Q) | 50S ribosomal protein L23 | polymer | 93 | 10336.9 | 1 | UniProt (Q9RXK0) Pfam (PF00276) | Deinococcus radiodurans | |
| 19 | S (R) | 50S ribosomal protein L24 | polymer | 110 | 11770.7 | 1 | UniProt (Q9RXJ1) Pfam (PF00467) Pfam (PF17136) | Deinococcus radiodurans | |
| 20 | T (S) | 50S ribosomal protein L25 | polymer | 175 | 19184.0 | 1 | UniProt (Q9RX88) Pfam (PF01386) Pfam (PF14693) | Deinococcus radiodurans | General stress protein CTC |
| 21 | U (T) | 50S ribosomal protein L27 | polymer | 84 | 8891.3 | 1 | UniProt (Q9RY65) Pfam (PF01016) | Deinococcus radiodurans | |
| 22 | V (U) | 50S ribosomal protein L28 | polymer | 72 | 7872.2 | 1 | UniProt (Q9RRG8) Pfam (PF00830) | Deinococcus radiodurans | |
| 23 | W (V) | 50S ribosomal protein L29 | polymer | 66 | 7646.9 | 1 | UniProt (Q9RXJ4) Pfam (PF00831) | Deinococcus radiodurans | |
| 24 | X (W) | 50S ribosomal protein L30 | polymer | 55 | 6079.2 | 1 | UniProt (Q9RSL0) Pfam (PF00327) | Deinococcus radiodurans | |
| 25 | Y (Z) | 50S ribosomal protein L32 | polymer | 57 | 6508.6 | 1 | UniProt (P49228) Pfam (PF01783) | Deinococcus radiodurans | |
| 26 | Z (1) | 50S ribosomal protein L33 | polymer | 54 | 5736.6 | 1 | UniProt (Q9RSS4) Pfam (PF00471) | Deinococcus radiodurans | |
| 27 | AA (2) | 50S ribosomal protein L34 | polymer | 47 | 5626.6 | 1 | UniProt (Q9RSH2) Pfam (PF00468) | Deinococcus radiodurans | |
| 28 | BA (3) | 50S ribosomal protein L35 | polymer | 65 | 7316.9 | 1 | UniProt (Q9RSW6) Pfam (PF01632) | Deinococcus radiodurans | |
| 29 | CA (X) | 23S ribosomal RNA | polymer | 2881 | 933750.3 | 1 | GenBank (11612676) | Deinococcus radiodurans | |
| 30 | DA (Y) | 5S ribosomal RNA | polymer | 122 | 39276.5 | 1 | GenBank (11612676) | Deinococcus radiodurans | |
| 31 | AB, AC, AD, AE, AF... (X, A, Y, H, M...) | MAGNESIUM ION | non-polymer | 24.3 | 186 | Chemie (MG) | |||
| 32 | DH (X) | Hygromycin A | non-polymer | 511.5 | 1 | Chemie (HGR) |
Sequence modifications
A: 2 - 275 (UniProt: Q9RXJ9)
F: 1 - 144 (UniProt: Q9RSS7)
L: 8 - 111 (UniProt: Q9RSL2)
M: 2 - 110 (UniProt: Q9RWB4)
U: 8 - 79 (UniProt: Q9RRG8)
1: 2 - 50 (UniProt: Q9RSS4)
X: 0 - 2880 (GenBank: 11612676)
| PDB | External Database | Details |
|---|---|---|
| Lys 7 | Arg 7 | conflict |
| Ala 25 | Thr 25 | conflict |
| Leu 270 | Ile 270 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 2 | Lys 2 | conflict |
| Arg 3 | Lys 3 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Lys 26 | Arg 26 | conflict |
| PDB | External Database | Details |
|---|---|---|
| - | Leu 107 | deletion |
| - | Arg 108 | deletion |
| - | Glu 109 | deletion |
| - | Leu 110 | deletion |
| PDB | External Database | Details |
|---|---|---|
| Ile 67 | Leu 67 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ala 0 | - | insertion |
| Ala 1 | - | insertion |
| Gly 3 | Lys 3 | conflict |
| Ala 4 | Asp 4 | conflict |
| Ala 5 | Gly 5 | conflict |
| Ala 45 | Lys 45 | conflict |
| His 46 | Lys 46 | conflict |
| Val 47 | His 47 | conflict |
| Phe 49 | Val 49 | conflict |
| Ala 50 | Phe 50 | conflict |
| Ala 51 | - | insertion |
| Ala 52 | - | insertion |
| Ala 53 | - | insertion |
| PDB | External Database | Details |
|---|---|---|
| U 1526 | Unk 2586412 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 30 |
| Total formula weight | 1355525.2 | |
| Non-Polymers* | Number of molecules | 187 |
| Total formula weight | 5032.2 | |
| All* | Total formula weight | 1360557.4 |
