MolNFT v1 · #151958 · protein
Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate
6I35 · Glycine dehydrogenase (decarboxylating), mitochondrial: “Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate”. X-ray diffraction, 2 ligands (PLG, BCT), 20 pockets (best…
- PDB
- 6I35
- Type
- protein
- Length
- 3,814 residues
- Chains
- 4
- 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
- PLG, BCT
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) | protein | 953 | 45% helix, 13% strand | P23378 |
| B, D | Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) | protein | 954 | 45% helix, 12% strand | P23378 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 4 copies · chains A, B, C, D
- BCT · Bicarbonate ion · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.85 | 0.86 | 85 | PEG |
| 2 | 1079 | 0.84 | 0.85 | 110 | EDO, GOL |
| 3 | 1071 | 0.84 | 0.85 | 116 | GOL, EDO |
| 4 | 1122 | 0.84 | 0.85 | 101 | EDO, PEG |
| 5 | 311 | 0.72 | 0.85 | 51 | PLG, GOL |
Interfaces
2 interfaces between chains.
- A–B · 3973 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 3966 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 6I35 · Crystal structure of human glycine decarboxylase (P-protein) bound with… · the same entry in another collection · chain D against D, TM-score 1.00
- P23378 · AlphaFold monomer V2.0 prediction for glycine dehydrogenase (decarboxylating)… · a predicted model of the same protein · chain D 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 6I35 · PDBe 6I35 · UniProt P23378
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