Research workbench
Crystal structure of a putative D-serine deaminase (BXE_A4060) from burkholderia xenovorans LB400 at 2.00 a resolution
Analyse Crystal structure of a putative D-serine deaminase (BXE_A4060) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GWQ
- Type
- protein
- Length
- 803 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-serine deaminase
- EC
- 4.3.1.18
- UniProt
- Q145Q0
- Ligands
- NA
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-serine deaminase (EC 4.3.1.18) | protein | 407 | 34% helix, 25% strand | Q145Q0 |
| B | D-serine deaminase (EC 4.3.1.18) | protein | 396 | 30% helix, 26% strand | Q145Q0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.81 | 0.98 | 63 | empty |
| 2 | 465 | 0.69 | 0.80 | 39 | NA |
| 3 | 179 | 0.66 | 0.86 | 24 | empty |
| 4 | 422 | 0.65 | 0.79 | 40 | GOL |
| 5 | 355 | 0.59 | 0.76 | 38 | GOL |
Interfaces
1 interface between chains.
- A–B · 3020 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3GWQ · Crystal structure of a putative d-serine deaminase (bxe_a4060) from burkholderia… · 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 Q145Q0
- Elsewhere: RCSB PDB 3GWQ · PDBe 3GWQ · UniProt Q145Q0
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