Research workbench
Crystal structure of mg-ADP-bound seca from bacillus subtilis
Analyse Crystal structure of mg-ADP-bound seca from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M74
- Type
- protein
- Length
- 802 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Preprotein translocase seca
- UniProt
- P28366
- Ligands
- ADP, MG, SO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Preprotein translocase seca | protein | 802 | 52% helix, 11% strand | P28366 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.86 | 0.87 | 93 | empty |
| 2 | 357 | 0.60 | 0.77 | 45 | SO4 |
| 3 | 284 | 0.60 | 0.79 | 34 | MG, ADP |
| 4 | 148 | 0.52 | 0.80 | 24 | empty |
| 5 | 168 | 0.47 | 0.76 | 18 | SO4 |
Compared structures
- 1M74 · Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis · 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 0.95
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 1M74 · PDBe 1M74 · UniProt P28366
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