Research workbench
N-terminal thioester domain of surface protein from clostridium perfringens
Analyse N-terminal thioester domain of surface protein from clostridium perfringens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A0G
- Type
- protein
- Length
- 1,052 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface anchored protein
- UniProt
- B1R775
- Pockets
- 15 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Surface anchored protein | protein | 175 | 32% helix, 19% strand | B1R775 |
| B | Surface anchored protein | protein | 176 | 32% helix, 19% strand | B1R775 |
| C | Surface anchored protein | protein | 176 | 32% helix, 19% strand | B1R775 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.66 | 0.75 | 58 | empty |
| 2 | 550 | 0.63 | 0.75 | 52 | empty |
| 3 | 397 | 0.56 | 0.74 | 40 | empty |
| 4 | 184 | 0.55 | 0.80 | 24 | empty |
| 5 | 261 | 0.53 | 0.76 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–D · 635 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 592 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 572 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 322 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 265 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5A0G · N-terminal thioester domain of surface protein from Clostridium perfringens · 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 B1R775
- Elsewhere: RCSB PDB 5A0G · PDBe 5A0G · UniProt B1R775
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