MolNFT v1 · #66309 · protein
Crystal structure of serine racemase
3HMK: “Crystal structure of serine racemase”. X-ray diffraction, 2 ligands (PLP, MN), 2 pockets (best druggability 0.80). MolNFT v1 #66309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HMK
- Type
- protein
- Length
- 643 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
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine racemase (EC 5.1.1.18) | protein | 321 | 46% helix, 16% strand | Q76EQ0 |
| B | Serine racemase (EC 5.1.1.18) | protein | 322 | 45% helix, 15% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.80 | 0.82 | 117 | PLP |
| 2 | 751 | 0.72 | 0.78 | 89 | PLP |
Interfaces
1 interface between chains.
- A–B · 740 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 3HMK · PDBe 3HMK · UniProt Q76EQ0
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