Research workbench
Structure of a human 48S translational initiation complex - EIF2-tc
Analyse Structure of a human 48S translational initiation complex - EIF2-tc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YBV
- Type
- protein + RNA
- Length
- 847 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 2 subunit 2; Eukaryotic translation initiation…
- EC
- 3.6.5.3
- UniProt
- P20042, P05198, P41091
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| s | Eukaryotic translation initiation factor 2 subunit 2 | protein | 138 | 31% helix, 11% strand | P20042 |
| r | Eukaryotic translation initiation factor 2 subunit 1 | protein | 275 | 39% helix, 18% strand | P05198 |
| w | Initiator methionine tRNA | rna | 75 | — | — |
| k | MRNA | rna | 3 | — | — |
| t | Eukaryotic translation initiation factor 2 subunit 3 (EC 3.6.5.3) | protein | 356 | 20% helix, 29% strand | P41091 |
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.84 | 0.85 | 147 | empty |
| 2 | 649 | 0.78 | 0.83 | 82 | empty |
| 3 | 469 | 0.75 | 0.84 | 68 | empty |
| 4 | 487 | 0.68 | 0.79 | 57 | empty |
| 5 | 517 | 0.66 | 0.78 | 52 | empty |
Interfaces
5 interfaces between chains.
- r–w · 901 Ų buried · 14 hydrogen bonds · protein-nucleic
- s–t · 552 Ų buried · 3 hydrogen bonds · protein-protein
- w–t · 341 Ų buried · 8 hydrogen bonds · protein-nucleic
- r–t · 341 Ų buried · 0 hydrogen bonds · protein-protein
- s–w · 318 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6YBV · Structure of a human 48S translational initiation complex - eIF2-TC · the same entry in another collection · chain t against t, TM-score 1.00
- P41091 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain t against A, TM-score 0.94
- P05198 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain r against A, TM-score 0.88
- P20042 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain s against A, TM-score 0.81
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 P20042
- Every structure of UniProt P05198
- Every structure of UniProt P41091
- Elsewhere: RCSB PDB 6YBV · PDBe 6YBV · UniProt P20042 · UniProt P05198 · UniProt P41091
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