Research workbench
Crystal structure of dimer of scpb N-terminal domain complexed with scpa peptide
Analyse Crystal structure of dimer of scpb N-terminal domain complexed with scpa peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W6K
- Type
- protein
- Length
- 365 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scpa; Scpb
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scpa | protein | 15 | 0% helix, 20% strand | — |
| B | Scpb | protein | 82 | 62% helix, 16% strand | — |
| C | Scpb | protein | 87 | 55% helix, 18% strand | — |
| D | Scpa | protein | 16 | 0% helix, 6% strand | — |
| E | Scpb | protein | 81 | 62% helix, 16% strand | — |
| F | Scpb | protein | 84 | 57% helix, 17% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.79 | 0.82 | 62 | empty |
| 2 | 62 | 0.50 | 0.85 | 16 | empty |
| 3 | 80 | 0.50 | 0.84 | 19 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1531 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1477 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 738 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 700 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 398 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3W6K · Crystal structure of dimer of ScpB N-terminal domain complexed with ScpA peptide · 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
- Elsewhere: RCSB PDB 3W6K · PDBe 3W6K
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