Research workbench
Crystal structure of the isolated dead motor domains from escherichia COLI seca
Analyse Crystal structure of the isolated dead motor domains from escherichia COLI seca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BXZ
- Type
- protein
- Length
- 878 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Preprotein translocase subunit seca
- UniProt
- P10408
- Ligands
- SPD, ADP, MG
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Preprotein translocase subunit seca | protein | 438 | 47% helix, 14% strand | P10408 |
| B | Preprotein translocase subunit seca | protein | 440 | 46% helix, 14% strand | P10408 |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · chains A, B
- 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.70 | 0.79 | 61 | MG, ADP |
| 2 | 524 | 0.69 | 0.79 | 61 | MG, ADP |
| 3 | 188 | 0.49 | 0.77 | 30 | empty |
| 4 | 152 | 0.46 | 0.76 | 31 | empty |
| 5 | 120 | 0.42 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1047 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3BXZ · Crystal structure of the isolated DEAD motor domains from Escherichia coli SecA · the same entry in another collection · chain A against A, TM-score 1.00
- P10408 · AlphaFold monomer V2.0 prediction for protein translocase subunit seca (P10408) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P10408
- Elsewhere: RCSB PDB 3BXZ · PDBe 3BXZ · UniProt P10408
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