Research workbench
Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form
Analyse Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WYU
- Type
- protein
- Length
- 3,640 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine dehydrogenase (decarboxylating) subunit 1; Glycine dehydrogenase subunit 2…
- EC
- 1.4.4.2
- UniProt
- Q5SKW8, Q5SKW7
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Glycine dehydrogenase (decarboxylating) subunit 1 (EC 1.4.4.2) | protein | 437 | 43% helix, 15% strand | Q5SKW8 |
| B, D, F, H | Glycine dehydrogenase subunit 2 (P-protein) (EC 1.4.4.2) | protein | 473 | 40% helix, 11% strand | Q5SKW7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.87 | 0.88 | 96 | empty |
| 2 | 1104 | 0.86 | 0.87 | 103 | empty |
| 3 | 98 | 0.78 | 0.99 | 24 | empty |
| 4 | 415 | 0.77 | 0.86 | 61 | PLP |
| 5 | 90 | 0.77 | 0.99 | 23 | empty |
Interfaces
18 interfaces between chains.
- E–F · 8751 Ų buried · 105 hydrogen bonds · protein-protein
- A–B · 8717 Ų buried · 101 hydrogen bonds · protein-protein
- C–D · 8713 Ų buried · 108 hydrogen bonds · protein-protein
- G–H · 8703 Ų buried · 110 hydrogen bonds · protein-protein
- F–H · 1158 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1WYU · Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in… · the same entry in another collection · chain H against H, TM-score 1.00
- Q5SKW7 · AlphaFold monomer V2.0 prediction for probable glycine dehydrogenase (decarboxylating)… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5SKW8
- Every structure of UniProt Q5SKW7
- Elsewhere: RCSB PDB 1WYU · PDBe 1WYU · UniProt Q5SKW8 · UniProt Q5SKW7
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