Research workbench
Structure of peptidyl-alpha-hydroxyglycine alpha-amidating lyase (pal)
Analyse Structure of peptidyl-alpha-hydroxyglycine alpha-amidating lyase (pal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FVZ
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-glycine alpha-amidating monooxygenase
- EC
- 4.3.2.5
- UniProt
- P14925
- Ligands
- ZN, FE, CA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-glycine alpha-amidating monooxygenase (EC 4.3.2.5) | protein | 329 | 2% helix, 43% strand | P14925 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- FE · Fe (III) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.68 | 0.81 | 43 | CA |
| 2 | 147 | 0.43 | 0.76 | 21 | empty |
| 3 | 54 | 0.35 | 0.79 | 14 | empty |
| 4 | 51 | 0.29 | 0.76 | 12 | ACT |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3FVZ · Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) · the same entry in another collection · chain A against A, TM-score 1.00
- P14925 · AlphaFold monomer V2.0 prediction for peptidylglycine alpha-amidating monooxygenase… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P14925
- Elsewhere: RCSB PDB 3FVZ · PDBe 3FVZ · UniProt P14925
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