MolNFT v1 · #170182 · protein + RNA
E. COLI 50S ribosomal subunit in complex with dirithromycin, fmet-phe- TRNA(PHE) and deacylated TRNA(IMET).
6XZ7 · 23S rRNA: “E. COLI 50S ribosomal subunit in complex with dirithromycin, fmet-phe- TRNA(PHE) and deacylated TRNA(IMET).”. Electron microscopy, 3 ligands (31M, DI0, MG), 20 pockets (best druggability 0.88). MolNFT v1 #170182 on…
- PDB
- 6XZ7
- Type
- protein + RNA
- Length
- 6,519 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
- UniProt
- P60422, P60438, P60723, P62399, P0AG55, P0A7J3, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6
- Ligands
- 31M, DI0, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 33 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2897 | — | — |
| B | 5S rRNA | rna | 120 | — | — |
| C | 50S ribosomal protein L2 | protein | 271 | 8% helix, 30% strand | P60422 |
| D | 50S ribosomal protein L3 | protein | 209 | 11% helix, 37% strand | P60438 |
| E | 50S ribosomal protein L4 | protein | 201 | 36% helix, 12% strand | P60723 |
| F | 50S ribosomal protein L5 | protein | 177 | 35% helix, 22% strand | P62399 |
| G | 50S ribosomal protein L6 | protein | 176 | 18% helix, 36% strand | P0AG55 |
| H | 50S ribosomal protein L10 | protein | 135 | 49% helix, 16% strand | P0A7J3 |
| I | 50S ribosomal protein L11 | protein | 134 | 40% helix, 17% strand | P0A7J7 |
| J | 50S ribosomal protein L13 | protein | 142 | 35% helix, 19% strand | P0AA10 |
| K | 50S ribosomal protein L14 | protein | 123 | 7% helix, 39% strand | P0ADY3 |
| L | 50S ribosomal protein L15 | protein | 144 | 19% helix, 14% strand | P02413 |
| M | 50S ribosomal protein L16 | protein | 136 | 19% helix, 28% strand | P0ADY7 |
| N | 50S ribosomal protein L17 | protein | 125 | 50% helix, 16% strand | P0AG44 |
| O | 50S ribosomal protein L18 | protein | 117 | 43% helix, 20% strand | P0C018 |
| P | 50S ribosomal protein L19 | protein | 114 | 18% helix, 43% strand | P0A7K6 |
| Q | 50S ribosomal protein L20 | protein | 117 | 79% helix, 0% strand | P0A7L3 |
| R | 50S ribosomal protein L21 | protein | 103 | 0% helix, 65% strand | P0AG48 |
| S | 50S ribosomal protein L22 | protein | 110 | 41% helix, 35% strand | P61175 |
| T | 50S ribosomal protein L23 | protein | 93 | 29% helix, 38% strand | P0ADZ0 |
| U | 50S ribosomal protein L24 | protein | 102 | 6% helix, 49% strand | P60624 |
| V | 50S ribosomal protein L25 | protein | 94 | 21% helix, 47% strand | P68919 |
| W | 50S ribosomal protein L27 | protein | 76 | 0% helix, 41% strand | P0A7L8 |
| X | 50S ribosomal protein L28 | protein | 77 | 27% helix, 36% strand | P0A7M2 |
| Y | 50S ribosomal protein L29 | protein | 62 | 79% helix, 0% strand | P0A7M6 |
| Z | 50S ribosomal protein L30 | protein | 58 | 33% helix, 26% strand | P0AG51 |
| a | 50S ribosomal protein L32 | protein | 56 | 18% helix, 13% strand | P0A7N4 |
| b | 50S ribosomal protein L33 | protein | 51 | 0% helix, 55% strand | P0A7N9 |
| c | 50S ribosomal protein L34 | protein | 46 | 54% helix, 0% strand | P0A7P5 |
| d | 50S ribosomal protein L35 | protein | 64 | 31% helix, 11% strand | P0A7Q1 |
| e | 50S ribosomal protein L36 | protein | 38 | 8% helix, 47% strand | P0A7Q6 |
| f | Deacylated TRNAI(MET) | rna | 76 | — | — |
| g | Fmet-phe-TRNA(PHE) | rna | 75 | — | — |
Ligands and binding sites
- 31M · 3'-deoxy-3'-[(L-methionyl-L-phenylalanyl) amino]adenosine 5'-(dihydrogen phosphate) · ligand · chains A, f, g
- DI0 · Dirithromycin · ligand · chains A, S
- MG · Magnesium ion · metal · 178 copies · chains A, E, L, C, d, J, N, D, c, T, B, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.88 | 0.90 | 106 | MG |
| 2 | 1053 | 0.87 | 0.89 | 116 | MG |
| 3 | 981 | 0.87 | 0.89 | 84 | MG |
| 4 | 859 | 0.86 | 0.90 | 79 | MG |
| 5 | 1073 | 0.86 | 0.88 | 88 | MG |
Interfaces
63 interfaces between chains.
- A–C · 7127 Ų buried · 193 hydrogen bonds · protein-nucleic
- A–D · 5063 Ų buried · 114 hydrogen bonds · protein-nucleic
- A–L · 4450 Ų buried · 112 hydrogen bonds · protein-nucleic
- A–E · 4131 Ų buried · 97 hydrogen bonds · protein-nucleic
- A–Q · 4082 Ų buried · 114 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 44 modified, 1 covalent (nucleotide modification, nonstandard, covalent ligand).
Compared structures
- 6XZ7 · E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P60422
- Every structure of UniProt P60438
- Every structure of UniProt P60723
- Every structure of UniProt P62399
- Every structure of UniProt P0AG55
- Every structure of UniProt P0A7J3
- Every structure of UniProt P0A7J7
- Every structure of UniProt P0AA10
- Every structure of UniProt P0ADY3
- Every structure of UniProt P02413
- Every structure of UniProt P0ADY7
- Every structure of UniProt P0AG44
- Every structure of UniProt P0C018
- Every structure of UniProt P0A7K6
- Every structure of UniProt P0A7L3
- Every structure of UniProt P0AG48
- Every structure of UniProt P61175
- Every structure of UniProt P0ADZ0
- Every structure of UniProt P60624
- Every structure of UniProt P68919
- Every structure of UniProt P0A7L8
- Every structure of UniProt P0A7M2
- Every structure of UniProt P0A7M6
- Every structure of UniProt P0AG51
- Every structure of UniProt P0A7N4
- Every structure of UniProt P0A7N9
- Every structure of UniProt P0A7P5
- Every structure of UniProt P0A7Q1
- Every structure of UniProt P0A7Q6
- Elsewhere: RCSB PDB 6XZ7 · PDBe 6XZ7 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0A7J3 · UniProt P0A7J7 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0ADY7 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P68919 · UniProt P0A7L8 · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt P0A7Q6
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