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 | 0 | 50S ribosomal protein L1 | polymer | 224 | 23514.9 | 1 | UniProt (Q9RSS8) Pfam (PF00687) In PDB | Deinococcus radiodurans | |
2 | A | 50S ribosomal protein L2 | polymer | 274 | 29918.5 | 1 | UniProt (Q9RXJ9) Pfam (PF00181) Pfam (PF03947) In PDB | Deinococcus radiodurans | |
3 | B | 50S ribosomal protein L3 | polymer | 205 | 21962.5 | 1 | UniProt (Q9RXK2) Pfam (PF00297) In PDB | Deinococcus radiodurans | |
4 | C | 50S ribosomal protein L4 | polymer | 197 | 21405.2 | 1 | UniProt (Q9RXK1) Pfam (PF00573) In PDB | Deinococcus radiodurans | |
5 | D | 50S ribosomal protein L5 | polymer | 177 | 19992.5 | 1 | UniProt (Q9RXJ0) Pfam (PF00673) Pfam (PF00281) In PDB | Deinococcus radiodurans | |
6 | E | 50S ribosomal protein L6 | polymer | 171 | 18266.0 | 1 | UniProt (Q9RSL3) Pfam (PF00347) In PDB | Deinococcus radiodurans | |
7 | F | 50S ribosomal protein L11 | polymer | 144 | 14945.2 | 1 | UniProt (Q9RSS7) Pfam (PF03946) Pfam (PF00298) In PDB | Deinococcus radiodurans | |
8 | G | 50S ribosomal protein L13 | polymer | 142 | 15837.3 | 1 | UniProt (Q9RXY1) Pfam (PF00572) In PDB | Deinococcus radiodurans | |
9 | H | 50S ribosomal protein L14 | polymer | 134 | 14256.5 | 1 | UniProt (Q9RXJ2) Pfam (PF00238) In PDB | Deinococcus radiodurans | |
10 | I | 50S ribosomal protein L15 | polymer | 141 | 15177.3 | 1 | UniProt (Q9RSK9) Pfam (PF00828) In PDB | Deinococcus radiodurans | |
11 | J | 50S ribosomal protein L16 | polymer | 136 | 15543.2 | 1 | UniProt (Q9RXJ5) Pfam (PF00252) In PDB | Deinococcus radiodurans | |
12 | K | 50S ribosomal protein L17 | polymer | 113 | 12538.5 | 1 | UniProt (Q9RSJ5) Pfam (PF01196) In PDB | Deinococcus radiodurans | |
13 | L | 50S ribosomal protein L18 | polymer | 104 | 11070.7 | 1 | UniProt (Q9RSL2) Pfam (PF00861) In PDB | Deinococcus radiodurans | |
14 | M | 50S ribosomal protein L19 | polymer | 109 | 12290.0 | 1 | UniProt (Q9RWB4) Pfam (PF01245) In PDB | Deinococcus radiodurans | |
15 | N | 50S ribosomal protein L20 | polymer | 117 | 13860.1 | 1 | UniProt (Q9RSW7) Pfam (PF00453) In PDB | Deinococcus radiodurans | |
16 | O | 50S ribosomal protein L21 | polymer | 94 | 10518.0 | 1 | UniProt (Q9RY64) Pfam (PF00829) In PDB | Deinococcus radiodurans | |
17 | P | 50S ribosomal protein L22 | polymer | 127 | 14432.0 | 1 | UniProt (Q9RXJ7) Pfam (PF00237) In PDB | Deinococcus radiodurans | |
18 | Q | 50S ribosomal protein L23 | polymer | 93 | 10336.9 | 1 | UniProt (Q9RXK0) Pfam (PF00276) In PDB | Deinococcus radiodurans | |
19 | R | 50S ribosomal protein L24 | polymer | 110 | 11770.7 | 1 | UniProt (Q9RXJ1) Pfam (PF00467) Pfam (PF17136) In PDB | Deinococcus radiodurans | |
20 | S | 50S ribosomal protein L25 | polymer | 175 | 19184.0 | 1 | UniProt (Q9RX88) Pfam (PF01386) Pfam (PF14693) In PDB | Deinococcus radiodurans | General stress protein CTC |
21 | T | 50S ribosomal protein L27 | polymer | 84 | 8891.3 | 1 | UniProt (Q9RY65) Pfam (PF01016) In PDB | Deinococcus radiodurans | |
22 | U | 50S ribosomal protein L28 | polymer | 72 | 7872.2 | 1 | UniProt (Q9RRG8) Pfam (PF00830) In PDB | Deinococcus radiodurans | |
23 | V | 50S ribosomal protein L29 | polymer | 66 | 7646.9 | 1 | UniProt (Q9RXJ4) Pfam (PF00831) In PDB | Deinococcus radiodurans | |
24 | W | 50S ribosomal protein L30 | polymer | 55 | 6079.2 | 1 | UniProt (Q9RSL0) Pfam (PF00327) In PDB | Deinococcus radiodurans | |
25 | Z | 50S ribosomal protein L32 | polymer | 57 | 6508.6 | 1 | UniProt (P49228) Pfam (PF01783) In PDB | Deinococcus radiodurans | |
26 | 1 | 50S ribosomal protein L33 | polymer | 54 | 5736.6 | 1 | UniProt (Q9RSS4) Pfam (PF00471) In PDB | Deinococcus radiodurans | |
27 | 2 | 50S ribosomal protein L34 | polymer | 47 | 5626.6 | 1 | UniProt (Q9RSH2) Pfam (PF00468) In PDB | Deinococcus radiodurans | |
28 | 3 | 50S ribosomal protein L35 | polymer | 65 | 7316.9 | 1 | UniProt (Q9RSW6) Pfam (PF01632) In PDB | Deinococcus radiodurans | |
29 | X | 23S ribosomal RNA | polymer | 2881 | 933750.3 | 1 | GenBank (11612676) | Deinococcus radiodurans | |
30 | Y | 5S ribosomal RNA | polymer | 122 | 39276.5 | 1 | GenBank (11612676) | Deinococcus radiodurans | |
31 | X, A, Y, H, M... | MAGNESIUM ION | non-polymer | 24.3 | 186 | Chemie (MG) | |||
32 | 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 |