MolNFT v1 · #39972 · protein
A novel dimer interface and conformational changes revealed by an X- ray structure of B. subtilis seca
2IBM · Preprotein translocase seca subunit: “A novel dimer interface and conformational changes revealed by an X- ray structure of B. subtilis seca”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #39972…
- PDB
- 2IBM
- Type
- protein
- Length
- 1,550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Preprotein translocase seca subunit
- UniProt
- P28366
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Preprotein translocase seca subunit | protein | 780 | 49% helix, 10% strand | P28366 |
| B | Preprotein translocase seca subunit | protein | 770 | 52% helix, 11% strand | P28366 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.86 | 0.87 | 138 | empty |
| 2 | 472 | 0.78 | 0.86 | 61 | empty |
| 3 | 474 | 0.77 | 0.85 | 54 | empty |
| 4 | 399 | 0.76 | 0.86 | 59 | empty |
| 5 | 437 | 0.75 | 0.84 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 3249 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2IBM · A novel dimer interface and conformational changes revealed by an X-ray structure of B.… · 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 B against A, TM-score 0.96
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 2IBM · PDBe 2IBM · UniProt P28366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.