MolNFT v1 · #17794 · protein
High resolution structure of oxidized active mutant of (S)-mandelate dehydrogenase
1P4C · L(+)-mandelate dehydrogenase: “High resolution structure of oxidized active mutant of (S)-mandelate dehydrogenase”. X-ray diffraction, 2 ligands (FMN, SO4), 5 pockets (best druggability 0.79). MolNFT v1 #17794 on GenesisL1: 3D…
- PDB
- 1P4C
- Type
- protein
- Length
- 353 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L(+)-mandelate dehydrogenase
- UniProt
- P20932, P05414
- Ligands
- FMN, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L(+)-mandelate dehydrogenase | protein | 353 | 45% helix, 13% strand | P20932, P05414 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.79 | 0.85 | 52 | SO4, FMN |
| 2 | 95 | 0.51 | 0.83 | 21 | empty |
| 3 | 76 | 0.36 | 0.77 | 18 | empty |
| 4 | 54 | 0.33 | 0.77 | 12 | empty |
| 5 | 67 | 0.29 | 0.73 | 15 | empty |
Compared structures
- 1P4C · High Resolution Structure of Oxidized Active Mutant of (S)-Mandelate Dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P20932 · AlphaFold monomer V2.0 prediction for (S)-mandelate dehydrogenase (P20932) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P05414 · AlphaFold monomer V2.0 prediction for peroxisomal (S)-2-hydroxy-acid oxidase (P05414) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P20932
- Every structure of UniProt P05414
- Elsewhere: RCSB PDB 1P4C · PDBe 1P4C · UniProt P20932 · UniProt P05414
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