MolNFT v1 · #151956 · protein
Crystal structure of human glycine decarboxylase (P-protein)
6I33 · Glycine dehydrogenase (decarboxylating), mitochondrial: “Crystal structure of human glycine decarboxylase (P-protein)”. X-ray diffraction, 2 ligands (PLP, BCT), 17 pockets (best druggability 0.85). MolNFT v1 #151956 on GenesisL1: 3D…
- PDB
- 6I33
- Type
- protein
- Length
- 1,875 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine dehydrogenase (decarboxylating), mitochondrial
- EC
- 1.4.4.2
- UniProt
- P23378
- Ligands
- PLP, BCT
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) | protein | 950 | 44% helix, 12% strand | P23378 |
| B | Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) | protein | 925 | 44% helix, 12% strand | P23378 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.85 | 0.86 | 127 | EDO |
| 2 | 943 | 0.84 | 0.85 | 81 | EDO |
| 3 | 355 | 0.67 | 0.81 | 43 | empty |
| 4 | 319 | 0.66 | 0.81 | 41 | empty |
| 5 | 166 | 0.52 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4028 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6I33 · Crystal structure of human glycine decarboxylase (P-protein) · the same entry in another collection · chain A against A, TM-score 1.00
- P23378 · AlphaFold monomer V2.0 prediction for glycine dehydrogenase (decarboxylating)… · a predicted model of the same protein · chain B 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 P23378
- Elsewhere: RCSB PDB 6I33 · PDBe 6I33 · UniProt P23378
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