Research workbench
Crystal structure of holo D-serine dehydratase from escherichia COLI at 1.55 a resolution
Analyse Crystal structure of holo D-serine dehydratase from escherichia COLI at 1.55 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SS7
- Type
- protein
- Length
- 437 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-serine dehydratase
- EC
- 4.3.1.18
- UniProt
- P00926
- Ligands
- PLP, K
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | D-serine dehydratase (EC 4.3.1.18) | protein | 437 | 56% helix, 14% strand | P00926 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains X
- K · Potassium ion · metal · chains X
- GOL · Glycerol · additive · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.67 | 0.81 | 45 | PLP |
| 2 | 100 | 0.45 | 0.79 | 27 | empty |
| 3 | 54 | 0.30 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3SS7 · Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.55 A resolution · the same entry in another collection · chain X against X, TM-score 1.00
- P00926 · AlphaFold monomer V2.0 prediction for D-serine dehydratase (P00926) · a predicted model of the same protein · chain X against A, TM-score 0.98
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 P00926
- Elsewhere: RCSB PDB 3SS7 · PDBe 3SS7 · UniProt P00926
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