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Dsba substrate complex
Analyse Dsba substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DKS
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsba; Siga peptide
- EC
- 1.8.4.2
- UniProt
- P52235
- Ligands
- ACE, HSE
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsba (EC 1.8.4.2) | protein | 188 | 54% helix, 11% strand | P52235 |
| B, C | THIOL:DISULFIDE interchange protein dsba (EC 1.8.4.2) | protein | 187 | 55% helix, 11% strand | P52235 |
| D | THIOL:DISULFIDE interchange protein dsba (EC 1.8.4.2) | protein | 186 | 54% helix, 11% strand | P52235 |
| E, F | Siga peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, A, F
- HSE · L-homoserine · ligand · 2 copies · chains C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.68 | 0.84 | 41 | ACE |
| 2 | 248 | 0.66 | 0.83 | 37 | ACE |
| 3 | 236 | 0.57 | 0.78 | 41 | empty |
| 4 | 222 | 0.56 | 0.78 | 35 | empty |
| 5 | 249 | 0.51 | 0.75 | 35 | empty |
Interfaces
7 interfaces between chains.
- B–C · 815 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 793 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 355 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 329 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 284 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
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 P52235
- Elsewhere: RCSB PDB 3DKS · PDBe 3DKS · UniProt P52235
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