Research workbench
X-ray crystal structure of rat serine racemase in complex with malonate a potent inhibitor
Analyse X-ray crystal structure of rat serine racemase in complex with malonate a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L6C
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine racemase
- EC
- 5.1.1.18
- UniProt
- Q76EQ0
- Ligands
- PLP, MN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine racemase (EC 5.1.1.18) | protein | 322 | 47% helix, 16% strand | Q76EQ0 |
| B | Serine racemase (EC 5.1.1.18) | protein | 312 | 46% helix, 16% strand | Q76EQ0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MLI · Malonate ion · additive · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.76 | 0.98 | 29 | PLP, MLI |
| 2 | 578 | 0.74 | 0.81 | 64 | empty |
| 3 | 152 | 0.71 | 0.90 | 38 | PLP, MLI |
| 4 | 368 | 0.61 | 0.77 | 36 | empty |
| 5 | 77 | 0.52 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 730 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3L6C · X-ray crystal structure of rat serine racemase in complex with malonate a potent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q76EQ0 · AlphaFold monomer V2.0 prediction for serine racemase (Q76EQ0) · a predicted model of the same protein · 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 Q76EQ0
- Elsewhere: RCSB PDB 3L6C · PDBe 3L6C · UniProt Q76EQ0
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