MolNFT v1 · #26757 · protein
Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form
1WYV · Glycine dehydrogenase (decarboxylating) subunit 1: “Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form”. X-ray diffraction, 2 ligands (PLP, AOA), 20 pockets (best…
- PDB
- 1WYV
- 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
- Ligands
- PLP, AOA
- 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 | 42% helix, 15% strand | — |
| B, D, F, H | Glycine dehydrogenase subunit 2 (P-protein) (EC 1.4.4.2) | protein | 473 | 39% helix, 12% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- AOA · (aminooxy)acetic acid · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.87 | 0.88 | 106 | empty |
| 2 | 1193 | 0.86 | 0.87 | 111 | empty |
| 3 | 389 | 0.78 | 0.88 | 52 | PLP, AOA |
| 4 | 94 | 0.77 | 0.99 | 22 | empty |
| 5 | 430 | 0.77 | 0.86 | 56 | PLP, AOA |
Interfaces
17 interfaces between chains.
- G–H · 8756 Ų buried · 106 hydrogen bonds · protein-protein
- A–B · 8743 Ų buried · 109 hydrogen bonds · protein-protein
- E–F · 8743 Ų buried · 105 hydrogen bonds · protein-protein
- C–D · 8714 Ų buried · 108 hydrogen bonds · protein-protein
- F–H · 1157 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1WYV · Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 1WYV · PDBe 1WYV
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