MolNFT v1 · #115831 · protein
Structure of maize serine racemase
5CVC: “Structure of maize serine racemase”. X-ray diffraction, 2 ligands (PLP, MG), 6 pockets (best druggability 0.71). MolNFT v1 #115831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CVC
- Type
- protein
- Length
- 965 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine racemase
- UniProt
- F5CAQ9
- Ligands
- PLP, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine racemase | protein | 329 | 53% helix, 16% strand | F5CAQ9 |
| B | Serine racemase | protein | 318 | 48% helix, 16% strand | F5CAQ9 |
| C | Serine racemase | protein | 318 | 51% helix, 15% strand | F5CAQ9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.71 | 0.78 | 68 | empty |
| 2 | 436 | 0.69 | 0.80 | 49 | PLP |
| 3 | 446 | 0.68 | 0.80 | 52 | PLP |
| 4 | 239 | 0.64 | 0.82 | 35 | PLP |
| 5 | 152 | 0.46 | 0.76 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1515 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 469 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5CVC · Structure of maize serine racemase · 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 F5CAQ9
- Elsewhere: RCSB PDB 5CVC · PDBe 5CVC · UniProt F5CAQ9
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