Research workbench
Crystal structure of the protein-translocation complex formed by the secy channel and the seca ATPase
Analyse Crystal structure of the protein-translocation complex formed by the secy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DIN
- Type
- protein
- Length
- 2,666 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit seca; Preprotein translocase subunit secy; Preprotein…
- UniProt
- Q9X1R4, Q9X1I9, P35874, B1L914
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein translocase subunit seca | protein | 816 | 49% helix, 8% strand | Q9X1R4 |
| C, F | Preprotein translocase subunit secy | protein | 396 | 54% helix, 1% strand | Q9X1I9 |
| D, G | Preprotein translocase subunit sece | protein | 56 | 84% helix, 0% strand | P35874 |
| E, H | Preprotein translocase subunit secg | protein | 65 | 60% helix, 0% strand | B1L914 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.86 | 0.88 | 86 | empty |
| 2 | 732 | 0.85 | 0.88 | 80 | empty |
| 3 | 646 | 0.84 | 0.89 | 101 | empty |
| 4 | 415 | 0.84 | 0.92 | 61 | empty |
| 5 | 758 | 0.83 | 0.87 | 100 | empty |
Interfaces
11 interfaces between chains.
- A–C · 3430 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 3418 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1464 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1420 Ų buried · 5 hydrogen bonds · protein-protein
- F–H · 1347 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3DIN · Crystal structure of the protein-translocation complex formed by the SecY channel and the… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9X1R4 · AlphaFold monomer V2.0 prediction for protein translocase subunit seca (Q9X1R4) · a predicted model of the same protein · chain A against A, TM-score 0.81
- Q9X1I9 · AlphaFold monomer V2.0 prediction for protein translocase subunit secy (Q9X1I9) · a predicted model of the same protein · chain C against A, TM-score 0.81
- P35874 · AlphaFold monomer V2.0 prediction for protein translocase subunit sece (P35874) · a predicted model of the same protein · chain D against A, TM-score 0.66
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 Q9X1R4
- Every structure of UniProt Q9X1I9
- Every structure of UniProt P35874
- Every structure of UniProt B1L914
- Elsewhere: RCSB PDB 3DIN · PDBe 3DIN · UniProt Q9X1R4 · UniProt Q9X1I9 · UniProt P35874 · UniProt B1L914
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