MolNFT v1 · #64965 · protein
Crystal structures of the G81A mutant of the active chimera of (S)- mandelate dehydrogenase and its complex with two of its substrates
3GIY · (S)-mandelate dehydrogenase, peroxisomal (S)-2-hydroxy-acid…: “Crystal structures of the G81A mutant of the active chimera of (S)- mandelate dehydrogenase and its complex…”. X-ray diffraction, 1 ligand (FMN), 5 pockets (best…
- PDB
- 3GIY
- Type
- protein
- Length
- 353 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (S)-mandelate dehydrogenase, peroxisomal (S)-2-hydroxy-acid oxidase
- EC
- 1.1.99.31, 1.1.3.15
- UniProt
- P20932, P05414
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (S)-mandelate dehydrogenase, peroxisomal (S)-2-hydroxy-acid oxidase (EC 1.1.99.31, 1.1.3.15) | protein | 353 | 46% helix, 13% strand | P20932, P05414 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 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 | 580 | 0.79 | 0.85 | 51 | FMN |
| 2 | 93 | 0.52 | 0.83 | 21 | empty |
| 3 | 65 | 0.35 | 0.77 | 18 | empty |
| 4 | 58 | 0.32 | 0.76 | 14 | empty |
| 5 | 62 | 0.28 | 0.73 | 16 | empty |
Compared structures
- 3GIY · Crystal Structures of the G81A Mutant of the Active Chimera of (S)-Mandelate… · 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 3GIY · PDBe 3GIY · UniProt P20932 · UniProt P05414
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