Research workbench
Fitting of components with known structure into an 11.5 a cryo-EM MAP of the E.COLI 70S ribosome
Analyse Fitting of components with known structure into an 11.5 a cryo-EM MAP of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EG0
- Type
- protein
- Length
- 1,466 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (S4 ribosomal protein); Protein (S5 ribosomal protein); Protein (S6 ribosomal…
- UniProt
- P81288, P02357, P23370, P17291, P80378, P23828, P27150, P02391, P29395
- Ligands
- 4SU, H2U, OMC, 5MU, PSU
- Pockets
- 2 · best druggability 0.36
Structure
electron microscopy · 11 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (S4 ribosomal protein) | protein | 159 | 0% helix, 0% strand | P81288 |
| B | Protein (S5 ribosomal protein) | protein | 145 | 0% helix, 0% strand | P02357 |
| C | Protein (S6 ribosomal protein) | protein | 97 | 0% helix, 0% strand | P23370 |
| D | Protein (S7 ribosomal protein) | protein | 135 | 0% helix, 0% strand | P17291 |
| E | Protein (S8 ribosomal protein) | protein | 136 | 0% helix, 0% strand | — |
| F | Protein (S15 ribosomal protein) | protein | 88 | 0% helix, 0% strand | P80378 |
| G | Protein (S17 ribosomal protein) | protein | 89 | 0% helix, 0% strand | P23828 |
| H | Protein (S20 ribosomal protein) | protein | 100 | 0% helix, 0% strand | — |
| N | Protein (ribosomal protein L1) | protein | 220 | 0% helix, 0% strand | P27150 |
| J | Protein (ribosomal protein L6) | protein | 164 | 0% helix, 0% strand | P02391 |
| K | Protein (ribosomal protein L11) | protein | 133 | 0% helix, 0% strand | P29395 |
Ligands and binding sites
- 4SU · 4-thiouridine-5'-monophosphate · ion
- H2U · 5,6-dihydrouridine-5'-monophosphate · ion
- OMC · O2'-methylycytidine-5'-monophosphate · ion
- 5MU · 5-methyluridine 5'-monophosphate · ion
- PSU · Pseudouridine-5'-monophosphate · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.36 | 0.73 | 21 | empty |
| 2 | 89 | 0.34 | 0.72 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 134 Ų buried · 0 hydrogen bonds · protein-protein
- E–G · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1EG0 · Fitting of components with known structure into an 11.5 a cryo-EM MAP of the E.COLI 70S… · the same entry in another collection · chain K against K, TM-score 1.00
- 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain K 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 P81288
- Every structure of UniProt P02357
- Every structure of UniProt P23370
- Every structure of UniProt P17291
- Every structure of UniProt P80378
- Every structure of UniProt P23828
- Every structure of UniProt P27150
- Every structure of UniProt P02391
- Every structure of UniProt P29395
- Elsewhere: RCSB PDB 1EG0 · PDBe 1EG0 · UniProt P81288 · UniProt P02357 · UniProt P23370 · UniProt P17291 · UniProt P80378 · UniProt P23828 · UniProt P27150 · UniProt P02391 · UniProt P29395
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