Research workbench
Cryo-EM structure of the mammalian SEC61 complex bound to the actively translating wheat germ 80S ribosome
Analyse Cryo-EM structure of the mammalian SEC61 complex bound to the actively… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WWB
- Type
- protein + RNA
- Length
- 1,591 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 6.48
- Source
- CANIS LUPUS FAMILIARIS; TRITICUM AESTIVUM
- Molecule
- Protein transport protein SEC61 subunit alpha isoform 1; Protein transport protein SEC61…
- UniProt
- P38377, P60058, P60467
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 6.48 · 15 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 subunit alpha isoform 1 | protein | 476 | 54% helix, 1% strand | P38377 |
| B | Protein transport protein SEC61 subunit gamma | protein | 68 | 63% helix, 0% strand | P60058 |
| C | Protein transport protein SEC61 subunit beta | protein | 36 | 42% helix, 0% strand | P60467 |
| D | 5.8S rRNA | rna | 63 | — | — |
| E | 25S rRNA | rna | 34 | — | — |
| F | 25S rRNA | rna | 25 | — | — |
| G | 25S rRNA | rna | 14 | — | — |
| H | 60S ribosomal protein L4-B | protein | 269 | 27% helix, 4% strand | — |
| I | 60S ribosomal protein L17-a | protein | 153 | 27% helix, 25% strand | — |
| J | 60S ribosomal protein L19 | protein | 53 | 47% helix, 8% strand | — |
| K | 60S ribosomal protein L25 | protein | 83 | 27% helix, 29% strand | — |
| L | 60S ribosomal protein L26-a | protein | 127 | 20% helix, 24% strand | — |
| M | 60S ribosomal protein L31-a | protein | 84 | 35% helix, 14% strand | — |
| N | 60S ribosomal protein L35 | protein | 69 | 64% helix, 0% strand | — |
| O | 60S ribosomal protein L39 | protein | 37 | 49% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.85 | 0.86 | 87 | empty |
| 2 | 923 | 0.80 | 0.82 | 89 | empty |
| 3 | 1162 | 0.80 | 0.82 | 71 | empty |
| 4 | 615 | 0.75 | 0.81 | 64 | empty |
| 5 | 454 | 0.73 | 0.83 | 44 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1650 Ų buried · 10 hydrogen bonds · protein-protein
- D–L · 1175 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–C · 1163 Ų buried · 13 hydrogen bonds · protein-protein
- D–N · 1007 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–O · 725 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 2WWB · Cryo-EM structure of the mammalian SEC61 complex bound to the actively translating wheat… · the same entry in another collection · chain O against O, 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 P38377
- Every structure of UniProt P60058
- Every structure of UniProt P60467
- Elsewhere: RCSB PDB 2WWB · PDBe 2WWB · UniProt P38377 · UniProt P60058 · UniProt P60467
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