Research workbench
Refined structures at 2 ångströms and 2.2 ångströms of the two forms of the H-protein, a lipoamide-containing protein of the glycine decarboxylase
Analyse Refined structures at 2 ångströms and 2.2 ångströms of the two forms of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HPC
- Type
- protein
- Length
- 262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H protein of the glycine cleavage system
- EC
- 1.4.4.2
- UniProt
- P16048
- Ligands
- LPB, LPA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | H protein of the glycine cleavage system (EC 1.4.4.2) | protein | 131 | 26% helix, 36% strand | P16048 |
Ligands and binding sites
- LPB · 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid · ligand · chains A, B
- LPA · Lipoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.69 | 0.97 | 22 | empty |
| 2 | 148 | 0.45 | 0.76 | 23 | LPB |
| 3 | 128 | 0.40 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (lipoylation).
Compared structures
- 1HPC · Refined structures at 2 ångströms and 2.2 ångströms of the two forms of the H-protein, a… · the same entry in another collection · chain A against A, TM-score 1.00
- P16048 · AlphaFold monomer V2.0 prediction for glycine cleavage system H protein, mitochondrial… · 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 P16048
- Elsewhere: RCSB PDB 1HPC · PDBe 1HPC · UniProt P16048
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