Research workbench
Crystal structure of DRP35, a 35KDA drug responsive protein from staphylococcus aureus, complexed with CA2+
Analyse Crystal structure of DRP35, a 35KDA drug responsive protein from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DG1
- Type
- protein
- Length
- 1,927 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DRP35
- EC
- 3.1.1.25
- UniProt
- Q9S0S3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | DRP35 (EC 3.1.1.25) | protein | 321 | 6% helix, 48% strand | Q9S0S3 |
| B | DRP35 (EC 3.1.1.25) | protein | 322 | 6% helix, 48% strand | Q9S0S3 |
| C | DRP35 (EC 3.1.1.25) | protein | 320 | 6% helix, 48% strand | Q9S0S3 |
| D | DRP35 (EC 3.1.1.25) | protein | 322 | 6% helix, 47% strand | Q9S0S3 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F
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 | 155 | 0.78 | 0.95 | 28 | GOL |
| 2 | 157 | 0.78 | 0.95 | 31 | GOL |
| 3 | 152 | 0.78 | 0.95 | 33 | GOL |
| 4 | 134 | 0.78 | 0.96 | 33 | GOL |
| 5 | 156 | 0.77 | 0.94 | 31 | GOL |
Interfaces
6 interfaces between chains.
- B–C · 1149 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1137 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 529 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 359 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 228 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2DG1 · Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9S0S3 · AlphaFold monomer V2.0 prediction for lactonase DRP35 (Q9S0S3) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q9S0S3
- Elsewhere: RCSB PDB 2DG1 · PDBe 2DG1 · UniProt Q9S0S3
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