Research workbench
Crystal structure of a calcium binding protein (BDI_1975) from parabacteroides distasonis atcc 8503 at 2.00 a resolution
Analyse Crystal structure of a calcium binding protein (BDI_1975) from parabacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U1W
- Type
- protein
- Length
- 748 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical periplasmic protein
- UniProt
- A6LDE6
- Ligands
- CA, CL
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical periplasmic protein | protein | 249 | 18% helix, 49% strand | A6LDE6 |
| C | Hypothetical periplasmic protein | protein | 250 | 17% helix, 50% strand | A6LDE6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C
- CL · Chloride ion · ion · 11 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, C
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.56 | 0.76 | 43 | empty |
| 2 | 286 | 0.50 | 0.73 | 38 | CL |
| 3 | 124 | 0.39 | 0.75 | 23 | empty |
| 4 | 129 | 0.38 | 0.74 | 24 | CA, EDO |
| 5 | 94 | 0.35 | 0.75 | 21 | ACT |
Interfaces
2 interfaces between chains.
- A–B · 910 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3U1W · Crystal structure of a Calcium binding protein (BDI_1975) from Parabacteroides distasonis… · 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 A6LDE6
- Elsewhere: RCSB PDB 3U1W · PDBe 3U1W · UniProt A6LDE6
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