Research workbench
Direct visualisation of strain-induced protein post- translational modification
Analyse Direct visualisation of strain-induced protein post- translational modification in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CRY
- Type
- protein
- Length
- 254 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate 1-decarboxylase; Panz
- EC
- 4.1.1.11
- UniProt
- P0A790, P37613
- Ligands
- ACO, MG, CL
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate 1-decarboxylase (EC 4.1.1.11) | protein | 25 | 0% helix, 64% strand | P0A790 |
| B | Panz | protein | 127 | 27% helix, 35% strand | P37613 |
| G | Aspartate 1-decarboxylase (EC 4.1.1.11) | protein | 102 | 16% helix, 45% strand | P0A790 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · chains B, G
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.63 | 0.80 | 38 | ACO, MG |
Interfaces
3 interfaces between chains.
- A–G · 1771 Ų buried · 45 hydrogen bonds · protein-protein
- B–G · 681 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, oxidation).
Compared structures
- 4CRY · Direct visualisation of strain-induced protein post-translational modification · the same entry in another collection · chain A against A, TM-score 1.00
- P0A790 · AlphaFold monomer V2.0 prediction for aspartate 1-decarboxylase (P0A790) · a predicted model of the same protein · chain G against A, TM-score 0.99
- P37613 · AlphaFold monomer V2.0 prediction for pand regulatory factor (P37613) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0A790
- Every structure of UniProt P37613
- Elsewhere: RCSB PDB 4CRY · PDBe 4CRY · UniProt P0A790 · UniProt P37613
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