2QEX
Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit
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 | 2772 | 897730.6 | 1 | Haloarcula marismortui | ||
2 | 9 | 5S ribosomal RNA | polymer | 122 | 39318.4 | 1 | GenBank (6468293) | Haloarcula marismortui | |
3 | A | 50S ribosomal protein L2P | polymer | 240 | 25354.7 | 1 | UniProt (P20276) Pfam (PF00181) Pfam (PF03947) In PDB | Haloarcula marismortui | |
4 | B | 50S ribosomal protein L3P | polymer | 338 | 37396.4 | 1 | UniProt (P20279) Pfam (PF00297) In PDB | Haloarcula marismortui | |
5 | C | 50S ribosomal protein L4P | polymer | 246 | 26442.1 | 1 | UniProt (P12735) Pfam (PF00573) In PDB | Haloarcula marismortui | |
6 | D | 50S ribosomal protein L5P | polymer | 177 | 19551.7 | 1 | UniProt (P14124) Pfam (PF00281) Pfam (PF00673) In PDB | Haloarcula marismortui | |
7 | E | 50S ribosomal protein L6P | polymer | 178 | 19961.7 | 1 | UniProt (P14135) Pfam (PF00347) In PDB | Haloarcula marismortui | |
8 | F | 50S ribosomal protein L7Ae | polymer | 120 | 12791.9 | 1 | UniProt (P12743) Pfam (PF01248) In PDB | Haloarcula marismortui | |
9 | G | Acidic ribosomal protein P0 homolog | polymer | 348 | 37213.8 | 1 | UniProt (P15825) Pfam (PF00466) Pfam (PF17777) In PDB | Haloarcula marismortui | |
10 | H | 50S ribosomal protein L10e | polymer | 174 | 19402.0 | 1 | UniProt (P60617) Pfam (PF00252) In PDB | Haloarcula marismortui | |
11 | J | 50S ribosomal protein L13P | polymer | 145 | 16249.2 | 1 | UniProt (P29198) Pfam (PF00572) In PDB | Haloarcula marismortui | |
12 | K | 50S ribosomal protein L14P | polymer | 132 | 14191.2 | 1 | UniProt (P22450) Pfam (PF00238) In PDB | Haloarcula marismortui | |
13 | L | 50S ribosomal protein L15P | polymer | 165 | 18005.4 | 1 | UniProt (P12737) Pfam (PF00828) In PDB | Haloarcula marismortui | |
14 | M | 50S ribosomal protein L15e | polymer | 196 | 22418.3 | 1 | UniProt (P60618) Pfam (PF00827) In PDB | Haloarcula marismortui | |
15 | N | 50S ribosomal protein L18P | polymer | 187 | 20640.9 | 1 | UniProt (P14123) Pfam (PF17144) In PDB | Haloarcula marismortui | |
16 | O | 50S ribosomal protein L18e | polymer | 116 | 12438.9 | 1 | UniProt (P12733) Pfam (PF00828) In PDB | Haloarcula marismortui | |
17 | P | 50S ribosomal protein L19e | polymer | 149 | 16796.5 | 1 | UniProt (P14119) Pfam (PF01280) In PDB | Haloarcula marismortui | |
18 | Q | 50S ribosomal protein L21e | polymer | 96 | 10567.8 | 1 | UniProt (P12734) Pfam (PF01157) In PDB | Haloarcula marismortui | |
19 | R | 50S ribosomal protein L22P | polymer | 155 | 16966.9 | 1 | UniProt (P10970) Pfam (PF00237) In PDB | Haloarcula marismortui | |
20 | S | 50S ribosomal protein L23P | polymer | 85 | 9612.5 | 1 | UniProt (P12732) Pfam (PF00276) In PDB | Haloarcula marismortui | |
21 | T | 50S ribosomal protein L24P | polymer | 120 | 13671.0 | 1 | UniProt (P10972) Pfam (PF16906) Pfam (PF00467) In PDB | Haloarcula marismortui | |
22 | U | 50S ribosomal protein L24e | polymer | 67 | 7364.9 | 1 | UniProt (P14116) Pfam (PF01246) In PDB | Haloarcula marismortui | |
23 | V | 50S ribosomal protein L29P | polymer | 71 | 7889.9 | 1 | UniProt (P10971) Pfam (PF00831) In PDB | Haloarcula marismortui | |
24 | W | 50S ribosomal protein L30P | polymer | 154 | 17062.9 | 1 | UniProt (P14121) Pfam (PF00327) In PDB | Haloarcula marismortui | |
25 | X | 50S ribosomal protein L31e | polymer | 92 | 10384.6 | 1 | UniProt (P18138) Pfam (PF01198) In PDB | Haloarcula marismortui | |
26 | Y | 50S ribosomal protein L32e | polymer | 241 | 26455.7 | 1 | UniProt (P12736) Pfam (PF14520) Pfam (PF01655) In PDB | Haloarcula marismortui | |
27 | Z | 50S ribosomal protein L37Ae | polymer | 73 | 8294.2 | 1 | UniProt (P60619) Pfam (PF01780) In PDB | Haloarcula marismortui | |
28 | 1 | 50S ribosomal protein L37e | polymer | 57 | 6330.2 | 1 | UniProt (P32410) Pfam (PF01907) In PDB | Haloarcula marismortui | |
29 | 2 | 50S ribosomal protein L39e | polymer | 50 | 6133.1 | 1 | UniProt (P22452) Pfam (PF00832) In PDB | Haloarcula marismortui | |
30 | 3 | 50S ribosomal protein L44e | polymer | 92 | 10815.2 | 1 | UniProt (P32411) Pfam (PF00935) In PDB | Haloarcula marismortui | |
31 | I | 50S ribosomal protein L11P | polymer | 162 | 17097.5 | 1 | UniProt (P14122) Pfam (PF03946) Pfam (PF00298) In PDB | Haloarcula marismortui | |
32 | 0, 3, K, 9, A... | MAGNESIUM ION | non-polymer | 24.3 | 116 | Chemie (MG) | |||
33 | 0 | POTASSIUM ION | non-polymer | 39.1 | 2 | Chemie (K) | |||
34 | 0, C, H, J, L... | SODIUM ION | non-polymer | 23.0 | 86 | Chemie (NA) | |||
35 | 3, J, 0, L, M... | CHLORIDE ION | non-polymer | 35.5 | 22 | Chemie (CL) | |||
36 | 0 | NEGAMYCIN | non-polymer | 248.3 | 1 | Chemie (NEG) | |||
37 | 3, O, U, Z, 1 | CADMIUM ION | non-polymer | 112.4 | 5 | Chemie (CD) | |||
38 | water | water | 18.0 | 7788 | Chemie (HOH) |
Sequence modifications
9: 3001 - 3122 (GenBank: 6468293)
C: 1 - 246 (UniProt: P12735)
G: 1 - 348 (UniProt: P15825)
H: -2 - 171 (UniProt: P60617)
K: 1 - 132 (UniProt: P22450)
M: 0 - 195 (UniProt: P60618)
Z: 10 - 82 (UniProt: P60619)
PDB | External Database | Details |
---|---|---|
G 3073 | A 215 | conflict |
C 3106 | U 248 | conflict |
PDB | External Database | Details |
---|---|---|
Leu 73 | Gln 73 | conflict |
PDB | External Database | Details |
---|---|---|
Asp 248 | Ala 248 | conflict |
PDB | External Database | Details |
---|---|---|
Asp 164 | - | insertion |
Ser 165 | Lys 167 | conflict |
Ser 166 | Val 168 | conflict |
Pro 167 | Glu 169 | conflict |
Ala 168 | Arg 170 | conflict |
- | Glu 172 | deletion |
- | Glu 173 | deletion |
- | Leu 174 | deletion |
- | Leu 175 | deletion |
Asn 170 | Ile 176 | conflict |
PDB | External Database | Details |
---|---|---|
Leu 44 | His 44 | conflict |
PDB | External Database | Details |
---|---|---|
Glu 13 | Lys 14 | conflict |
Ala 194 | Gly 195 | conflict |
PDB | External Database | Details |
---|---|---|
Arg 10 | Ser 10 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 31 |
Total formula weight | 1424550.3 | |
Non-Polymers* | Number of molecules | 232 |
Total formula weight | 6465.0 | |
All* | Total formula weight | 1431015.3 |