Research workbench
Fitting the ternary complex of ef-TU/TRNA/GTP and ribosomal proteins into a 13 a cryo-EM MAP of the COLI 70S ribosome
Analyse Fitting the ternary complex of ef-TU/TRNA/GTP and ribosomal proteins into a 13… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MJ1
- Type
- protein + RNA
- Length
- 939 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phe-tRNA; Elongation factor tu; S12 ribosomal protein; S13 ribosomal protein; L11…
- UniProt
- P0A7S3
- Pockets
- 10 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 13% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | Phe-tRNA | rna | 76 | — | — |
| A | Elongation factor tu | protein | 405 | 25% helix, 35% strand | — |
| O | S12 ribosomal protein | protein | 124 | 0% helix, 0% strand | P0A7S3 |
| P | S13 ribosomal protein | protein | 125 | 0% helix, 0% strand | — |
| L | L11 ribosomal protein | protein | 133 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.76 | 0.79 | 86 | empty |
| 2 | 742 | 0.75 | 0.81 | 79 | empty |
| 3 | 1131 | 0.71 | 0.76 | 113 | empty |
| 4 | 838 | 0.68 | 0.75 | 109 | empty |
| 5 | 628 | 0.62 | 0.75 | 32 | empty |
Interfaces
4 interfaces between chains.
- D–A · 474 Ų buried · 57 hydrogen bonds · protein-nucleic
- D–O · 427 Ų buried · 0 hydrogen bonds · protein-nucleic
- C–P · 98 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–O · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (nucleotide modification).
Compared structures
- 1MJ1 · FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM… · the same entry in another collection · chain D against D, 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 P0A7S3
- Elsewhere: RCSB PDB 1MJ1 · PDBe 1MJ1 · UniProt P0A7S3
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