MolNFT v1 · #26755 · protein
Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form
1WYT · Glycine dehydrogenase (decarboxylating) subunit 1: “Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form”. X-ray diffraction, 15 pockets (best druggability 0.85). MolNFT v1 #26755 on…
- PDB
- 1WYT
- Type
- protein
- Length
- 1,816 residues
- Chains
- 4
- 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
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycine dehydrogenase (decarboxylating) subunit 1 (EC 1.4.4.2) | protein | 437 | 41% helix, 15% strand | Q5SKW8 |
| B, D | Glycine dehydrogenase subunit 2 (P-protein) (EC 1.4.4.2) | protein | 471 | 39% helix, 11% strand | Q5SKW7 |
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.85 | 0.86 | 121 | empty |
| 2 | 89 | 0.77 | 0.99 | 26 | empty |
| 3 | 82 | 0.75 | 0.98 | 22 | empty |
| 4 | 701 | 0.75 | 0.81 | 67 | empty |
| 5 | 688 | 0.74 | 0.80 | 74 | empty |
Interfaces
6 interfaces between chains.
- A–B · 8419 Ų buried · 95 hydrogen bonds · protein-protein
- C–D · 8326 Ų buried · 93 hydrogen bonds · protein-protein
- B–D · 1130 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 793 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 741 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1WYT · 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
- 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 1WYT · PDBe 1WYT · UniProt Q5SKW8 · UniProt Q5SKW7
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