Research workbench
Crystal structure of B. subtilis seca with bound peptide
Analyse Crystal structure of B. subtilis seca with bound peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JV2
- Type
- protein
- Length
- 1,526 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit seca; Peptide
- UniProt
- P28366
- Ligands
- ADP, MG
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein translocase subunit seca | protein | 758 | 54% helix, 13% strand | P28366 |
| B | Protein translocase subunit seca | protein | 762 | 55% helix, 13% strand | P28366 |
| C, D | Peptide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · 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
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.73 | 0.79 | 79 | empty |
| 2 | 429 | 0.71 | 0.82 | 54 | MG, ADP |
| 3 | 329 | 0.68 | 0.82 | 39 | MG, ADP |
| 4 | 568 | 0.67 | 0.77 | 66 | empty |
| 5 | 367 | 0.65 | 0.80 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1193 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 187 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3JV2 · Crystal Structure of B. subtilis SecA with bound peptide · 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 0.85
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
- Elsewhere: RCSB PDB 3JV2 · PDBe 3JV2 · UniProt P28366
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