Research workbench
Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.
Analyse Computer-based redesign of a beta sandwich protein suggests that extensive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B83
- Type
- protein
- Length
- 761 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ten-D3
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ten-D3 | protein | 95 | 0% helix, 52% strand | — |
| B, F | Ten-D3 | protein | 92 | 0% helix, 53% strand | — |
| C, E, G | Ten-D3 | protein | 99 | 0% helix, 49% strand | — |
| D | Ten-D3 | protein | 91 | 0% helix, 54% strand | — |
| H | Ten-D3 | protein | 94 | 0% helix, 50% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.74 | 0.77 | 101 | empty |
| 2 | 267 | 0.51 | 0.75 | 41 | empty |
| 3 | 137 | 0.51 | 0.80 | 26 | empty |
| 4 | 82 | 0.42 | 0.80 | 17 | empty |
| 5 | 121 | 0.37 | 0.73 | 18 | empty |
Interfaces
14 interfaces between chains.
- C–D · 682 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 621 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 615 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 615 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 602 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3B83 · Computer-Based Redesign of a beta Sandwich Protein Suggests that Extensive Negative… · 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 3B83 · PDBe 3B83
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