MolNFT v1 · #98678 · protein
Crystal structure of glycine decarboxylase P-protein from synechocystis sp. pcc 6803, apo form
4LGL · Glycine dehydrogenase [decarboxylating]: “Crystal structure of glycine decarboxylase P-protein from synechocystis sp. pcc 6803, apo form”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.87). MolNFT v1 #98678 on…
- PDB
- 4LGL
- Type
- protein
- Length
- 1,878 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine dehydrogenase [decarboxylating]
- EC
- 1.4.4.2
- UniProt
- P74416
- Ligands
- CL
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine dehydrogenase [decarboxylating] (EC 1.4.4.2) | protein | 948 | 43% helix, 13% strand | P74416 |
| B | Glycine dehydrogenase [decarboxylating] (EC 1.4.4.2) | protein | 930 | 44% helix, 13% strand | P74416 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.87 | 0.89 | 120 | TRS |
| 2 | 1108 | 0.83 | 0.84 | 111 | empty |
| 3 | 116 | 0.78 | 0.98 | 32 | empty |
| 4 | 116 | 0.78 | 0.98 | 33 | empty |
| 5 | 96 | 0.77 | 0.98 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 4025 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (artifact, disulfide).
Compared structures
- P74416 · AlphaFold monomer V2.0 prediction for glycine dehydrogenase (decarboxylating) (P74416) · 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 P74416
- Elsewhere: RCSB PDB 4LGL · PDBe 4LGL · UniProt P74416
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