Research workbench
Crystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (phm) in complex with citrate
Analyse Crystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ALA
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-glycine alpha-amidating monooxygenase
- EC
- 1.14.17.3, 4.3.2.5
- UniProt
- P14925
- Ligands
- CU
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-glycine alpha-amidating monooxygenase (EC 1.14.17.3, 4.3.2.5) | protein | 297 | 7% helix, 49% strand | P14925 |
| C | Peptidyl-glycine alpha-amidating monooxygenase (EC 1.14.17.3, 4.3.2.5) | protein | 304 | 7% helix, 49% strand | P14925 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 13 copies · chains A, C
- FLC · Citrate anion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.71 | 0.79 | 67 | empty |
| 2 | 419 | 0.66 | 0.79 | 52 | empty |
| 3 | 456 | 0.64 | 0.77 | 40 | empty |
| 4 | 199 | 0.56 | 0.79 | 27 | CU, FLC, GOL |
| 5 | 197 | 0.54 | 0.78 | 30 | CU, FLC, GOL |
Interfaces
1 interface between chains.
- A–C · 584 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6ALA · Crystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (PHM) in… · 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 0.87
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 6ALA · PDBe 6ALA · UniProt P14925
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