Research workbench
N-terminal thioester domain of surface protein from clostridium perfringens, CYS138ALA mutant
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
- 5A0D
- Type
- protein
- Length
- 697 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface anchored protein
- UniProt
- B1R775
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Surface anchored protein | protein | 175 | 32% helix, 26% strand | B1R775 |
| B | Surface anchored protein | protein | 176 | 32% helix, 24% strand | B1R775 |
| C | Surface anchored protein | protein | 172 | 32% helix, 23% strand | B1R775 |
| D | Surface anchored protein | protein | 174 | 32% helix, 24% strand | B1R775 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.76 | 0.79 | 61 | EDO |
| 2 | 889 | 0.74 | 0.78 | 62 | EDO |
| 3 | 760 | 0.72 | 0.78 | 66 | empty |
| 4 | 438 | 0.71 | 0.81 | 55 | EDO |
| 5 | 669 | 0.71 | 0.78 | 59 | empty |
Interfaces
5 interfaces between chains.
- A–D · 864 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 785 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 276 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 245 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5A0D · N-terminal thioester domain of surface protein from Clostridium perfringens, Cys138Ala… · 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 5A0D · PDBe 5A0D · UniProt B1R775
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