Research workbench
Cryo-EM structure of idle yeast SSH1 complex bound to the yeast 80S ribosome
Analyse Cryo-EM structure of idle yeast SSH1 complex bound to the yeast 80S ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WWA
- Type
- protein + RNA
- Length
- 1,586 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sec sixty-one protein homolog; Protein transport protein SSS1; Protein transport protein…
- UniProt
- P38353, P35179, P52871, P49626, P05740, P05735, P04456, P05743, P0C2H8, P39741, P04650
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 15 distinct chains · 34% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sec sixty-one protein homolog | protein | 490 | 43% helix, 2% strand | P38353 |
| B | Protein transport protein SSS1 | protein | 60 | 60% helix, 0% strand | P35179 |
| C | Protein transport protein SEB2 | protein | 21 | 71% helix, 0% strand | P52871 |
| D | 25S rRNA | rna | 63 | — | — |
| E | 25S rRNA | rna | 34 | — | — |
| F | 25S rRNA | rna | 25 | — | — |
| G | 25S rRNA | rna | 18 | — | — |
| H | 60S ribosomal protein L4-B | protein | 269 | 21% helix, 8% strand | P49626 |
| I | 60S ribosomal protein L17-a | protein | 153 | 23% helix, 20% strand | P05740 |
| J | 60S ribosomal protein L19 | protein | 53 | 42% helix, 11% strand | P05735 |
| K | 60S ribosomal protein L25 | protein | 83 | 27% helix, 28% strand | P04456 |
| L | 60S ribosomal protein L26-a | protein | 127 | 18% helix, 21% strand | P05743 |
| M | 60S ribosomal protein L31-a | protein | 84 | 29% helix, 14% strand | P0C2H8 |
| N | 60S ribosomal protein L35 | protein | 69 | 46% helix, 0% strand | P39741 |
| O | 60S ribosomal protein L39 | protein | 37 | 35% helix, 0% strand | P04650 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.85 | 0.86 | 82 | empty |
| 2 | 863 | 0.80 | 0.84 | 52 | empty |
| 3 | 619 | 0.80 | 0.86 | 62 | empty |
| 4 | 522 | 0.69 | 0.79 | 41 | empty |
| 5 | 62 | 0.69 | 0.97 | 18 | empty |
Interfaces
26 interfaces between chains.
- A–B · 1642 Ų buried · 7 hydrogen bonds · protein-protein
- D–L · 1181 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–N · 1042 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 865 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 790 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- 2WWA · Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 80S ribosome · 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 P38353
- Every structure of UniProt P35179
- Every structure of UniProt P52871
- Every structure of UniProt P49626
- Every structure of UniProt P05740
- Every structure of UniProt P05735
- Every structure of UniProt P04456
- Every structure of UniProt P05743
- Every structure of UniProt P0C2H8
- Every structure of UniProt P39741
- Every structure of UniProt P04650
- Elsewhere: RCSB PDB 2WWA · PDBe 2WWA · UniProt P38353 · UniProt P35179 · UniProt P52871 · UniProt P49626 · UniProt P05740 · UniProt P05735 · UniProt P04456 · UniProt P05743 · UniProt P0C2H8 · UniProt P39741 · UniProt P04650
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