Research workbench
Cryo-EM structure of PCAT1 in the inward-facing intermediate conformation under ATP turnover condition
Analyse Cryo-EM structure of PCAT1 in the inward-facing intermediate conformation under… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T56
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type bacteriocin transporter; PCAT1 peptide substrate
- UniProt
- A3DCU1, A3DCU2
- Ligands
- ATP, MG
- Pockets
- 15 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC-type bacteriocin transporter | protein | 715 | 54% helix, 12% strand | A3DCU1 |
| C, D | PCAT1 peptide substrate | protein | 17 | 35% helix, 12% strand | A3DCU2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · 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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.78 | 0.80 | 128 | empty |
| 2 | 483 | 0.74 | 0.83 | 56 | empty |
| 3 | 241 | 0.73 | 0.87 | 33 | empty |
| 4 | 1075 | 0.72 | 0.76 | 116 | empty |
| 5 | 897 | 0.71 | 0.76 | 74 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5426 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 738 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 730 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7T56 · Cryo-EM structure of PCAT1 in the inward-facing intermediate conformation under ATP… · 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 A3DCU1
- Every structure of UniProt A3DCU2
- Elsewhere: RCSB PDB 7T56 · PDBe 7T56 · UniProt A3DCU1 · UniProt A3DCU2
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