Research workbench
Crystal structure of the seca protein translocation ATPase from mycobacterium tuberculosis complex with adpbs
Analyse Crystal structure of the seca protein translocation ATPase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NKT
- Type
- protein
- Length
- 1,672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Preprotein translocase seca 1 subunit
- UniProt
- P0A5Y8
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Preprotein translocase seca 1 subunit | protein | 836 | 56% helix, 11% strand | P0A5Y8 |
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
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.79 | 0.84 | 81 | MG, ADP |
| 2 | 644 | 0.78 | 0.83 | 85 | MG, ADP |
| 3 | 865 | 0.76 | 0.80 | 89 | empty |
| 4 | 646 | 0.74 | 0.80 | 77 | empty |
| 5 | 304 | 0.61 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1512 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1NKT · Crystal structure of the seca protein translocation ATPase from mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
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 P0A5Y8
- Elsewhere: RCSB PDB 1NKT · PDBe 1NKT · UniProt P0A5Y8
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