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Crystal structure of a putative protease (BDI_1141) from parabacteroides distasonis atcc 8503 at 2.00 a resolution
Analyse Crystal structure of a putative protease (BDI_1141) from parabacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KD4
- Type
- protein
- Length
- 1,010 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative protease
- UniProt
- A6LB40
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative protease | protein | 505 | 23% helix, 40% strand | A6LB40 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.76 | 0.79 | 96 | GOL |
| 2 | 896 | 0.75 | 0.78 | 80 | GOL |
| 3 | 201 | 0.62 | 0.83 | 40 | GOL |
| 4 | 220 | 0.62 | 0.82 | 37 | GOL |
| 5 | 86 | 0.41 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3KD4 · Crystal structure of a putative protease (BDI_1141) from parabacteroides distasonis atcc… · 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 A6LB40
- Elsewhere: RCSB PDB 3KD4 · PDBe 3KD4 · UniProt A6LB40
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