Research workbench
Oxidized (CU2+) peptidylglycine alpha-hydroxylating monooxygenase (phm) with bound nitrite, obtained in the presence of substrate
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
- 3MIG
- Type
- protein
- Length
- 309 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, NO2
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-glycine alpha-amidating monooxygenase (EC 1.14.17.3) | protein | 309 | 5% helix, 49% strand | P14925 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- NO2 · Nitrite ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 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 | 513 | 0.64 | 0.76 | 49 | NO2 |
| 2 | 65 | 0.56 | 0.88 | 18 | empty |
| 3 | 74 | 0.47 | 0.83 | 22 | GOL |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3MIG · Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound… · 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 3MIG · PDBe 3MIG · UniProt P14925
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