Research workbench
Oxidized (CU2+) peptidylglycine alpha-hydroxylating monooxygenase (phm) with bound azide obtained by soaking (100MM NAN3)
Analyse Oxidized (CU2+) peptidylglycine alpha-hydroxylating monooxygenase (phm) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MID
- Type
- protein
- Length
- 311 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-glycine alpha-amidating monooxygenase
- EC
- 1.14.17.3
- UniProt
- P14925
- Ligands
- CU, NI, AZI
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-glycine alpha-amidating monooxygenase (EC 1.14.17.3) | protein | 311 | 6% helix, 48% strand | P14925 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- AZI · Azide ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.63 | 0.76 | 45 | AZI |
| 2 | 89 | 0.58 | 0.87 | 21 | GOL |
| 3 | 75 | 0.48 | 0.83 | 20 | GOL |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3MID · Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide… · 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 0.99
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 3MID · PDBe 3MID · UniProt P14925
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