Research workbench
Crystal structure of a tpr-domain containing protein (BDI_1685) from parabacteroides distasonis atcc 8503 at 2.26 a resolution
Analyse Crystal structure of a tpr-domain containing protein (BDI_1685) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CD6
- Type
- protein
- Length
- 1,725 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tpr-domain containing protein
- UniProt
- A6LCM3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tpr-domain containing protein | protein | 575 | 27% helix, 27% strand | A6LCM3 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.78 | 0.80 | 65 | empty |
| 2 | 367 | 0.74 | 0.85 | 51 | empty |
| 3 | 364 | 0.74 | 0.85 | 44 | empty |
| 4 | 381 | 0.73 | 0.84 | 40 | empty |
| 5 | 1042 | 0.71 | 0.75 | 107 | CA |
Interfaces
3 interfaces between chains.
- A–B · 1931 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 150 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 5CD6 · Crystal structure of a TPR-domain containing protein (BDI_1685) from Parabacteroides… · 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 A6LCM3
- Elsewhere: RCSB PDB 5CD6 · PDBe 5CD6 · UniProt A6LCM3
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