Research workbench
Crystal structure of synechocystis sp. pcc 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine
Analyse Crystal structure of synechocystis sp. pcc 6803 glycine decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LHC
- Type
- protein
- Length
- 1,884 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
- GLY, BCT, BCN, PO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine dehydrogenase [decarboxylating] (EC 1.4.4.2) | protein | 942 | 45% helix, 13% strand | P74416 |
| B | Glycine dehydrogenase [decarboxylating] (EC 1.4.4.2) | protein | 942 | 45% helix, 13% strand | P74416 |
Ligands and binding sites
- GLY · Glycine · ligand · 5 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 3 copies · chains A, B
- BCN · Bicine · ligand · chains A
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.86 | 0.87 | 123 | BCT |
| 2 | 903 | 0.82 | 0.83 | 72 | EDO |
| 3 | 663 | 0.71 | 0.78 | 67 | GLY |
| 4 | 381 | 0.69 | 0.82 | 54 | empty |
| 5 | 371 | 0.68 | 0.82 | 53 | BCT |
Interfaces
1 interface between chains.
- A–B · 4099 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 4LHC · Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo… · the same entry in another collection · chain A against A, TM-score 1.00
- P74416 · AlphaFold monomer V2.0 prediction for glycine dehydrogenase (decarboxylating) (P74416) · a predicted model of the same protein · 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
- Every structure of UniProt P74416
- Elsewhere: RCSB PDB 4LHC · PDBe 4LHC · UniProt P74416
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.