Research workbench
Peptide-bound state of thermus thermophilus secyeg
Analyse Peptide-bound state of thermus thermophilus secyeg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CH4
- Type
- protein
- Length
- 555 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit secy; Protein translocase subunit sece; Putative preprotein…
- UniProt
- Q5SHQ8, P38383, Q5SHE6
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Protein translocase subunit secy | protein | 421 | 68% helix, 3% strand | Q5SHQ8 |
| E | Protein translocase subunit sece | protein | 60 | 70% helix, 2% strand | P38383 |
| G | Putative preprotein translocase, secg subunit | protein | 74 | 65% helix, 0% strand | Q5SHE6 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.63 | 0.88 | 18 | empty |
| 2 | 76 | 0.61 | 0.89 | 20 | empty |
| 3 | 273 | 0.56 | 0.77 | 31 | empty |
| 4 | 179 | 0.55 | 0.79 | 22 | empty |
| 5 | 136 | 0.54 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- Y–E · 1994 Ų buried · 9 hydrogen bonds · protein-protein
- Y–G · 1864 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CH4 · Peptide-Bound State of Thermus thermophilus SecYEG · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q5SHQ8 · AlphaFold monomer V2.0 prediction for protein translocase subunit secy (Q5SHQ8) · a predicted model of the same protein · chain Y against A, TM-score 0.97
- P38383 · AlphaFold monomer V2.0 prediction for protein translocase subunit sece (P38383) · a predicted model of the same protein · chain E against A, TM-score 0.76
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 Q5SHQ8
- Every structure of UniProt P38383
- Every structure of UniProt Q5SHE6
- Elsewhere: RCSB PDB 5CH4 · PDBe 5CH4 · UniProt Q5SHQ8 · UniProt P38383 · UniProt Q5SHE6
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