MolNFT v1 · #118195 · protein
Structure of the seca-secy complex with a translocating polypeptide substrate
5EUL · Protein translocase subunit seca, insertion peptide chimera: “Structure of the seca-secy complex with a translocating polypeptide substrate”. X-ray diffraction, 4 ligands (TBR, BEF, ADP), 18 pockets (best druggability 0.85). MolNFT…
- PDB
- 5EUL
- Type
- protein
- Length
- 1,297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit seca, insertion peptide chimera; Protein translocase subunit…
- UniProt
- P28366, A4IJK8, A4IJH4
- Ligands
- TBR, BEF, ADP, MG
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein translocase subunit seca, insertion peptide chimera | protein | 746 | 53% helix, 12% strand | P28366 |
| Y | Protein translocase subunit secy | protein | 380 | 62% helix, 4% strand | A4IJK8 |
| E | Preprotein translocase sece subunit | protein | 56 | 82% helix, 0% strand | A4IJH4 |
| V | AYC08 | protein | 115 | 3% helix, 46% strand | — |
Ligands and binding sites
- TBR · Hexatantalum dodecabromide · ligand · 18 copies · chains A, Y
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.85 | 0.89 | 88 | empty |
| 2 | 495 | 0.78 | 0.86 | 45 | TBR |
| 3 | 422 | 0.76 | 0.85 | 49 | MG, BEF, ADP |
| 4 | 666 | 0.75 | 0.81 | 67 | empty |
| 5 | 266 | 0.71 | 0.86 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–Y · 3991 Ų buried · 14 hydrogen bonds · protein-protein
- Y–E · 1593 Ų buried · 7 hydrogen bonds · protein-protein
- Y–V · 760 Ų buried · 9 hydrogen bonds · protein-protein
- A–V · 55 Ų buried · 0 hydrogen bonds · protein-protein
- E–V · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5EUL · Structure of the SecA-SecY complex with a translocating polypeptide substrate · the same entry in another collection · chain A against A, TM-score 1.00
- P28366 · AlphaFold monomer V2.0 prediction for protein translocase subunit seca (P28366) · a predicted model of the same protein · chain A 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 P28366
- Every structure of UniProt A4IJK8
- Every structure of UniProt A4IJH4
- Elsewhere: RCSB PDB 5EUL · PDBe 5EUL · UniProt P28366 · UniProt A4IJK8 · UniProt A4IJH4
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