Research workbench
Crystal structure of H107A peptidylglycine alpha-hydroxylating monooxygenase (phm) in complex with citrate
Analyse Crystal structure of H107A 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
- 5WJA
- Type
- protein
- Length
- 616 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, NI
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% 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 | 305 | 4% helix, 48% strand | P14925 |
| D | Peptidyl-glycine alpha-amidating monooxygenase (EC 1.14.17.3, 4.3.2.5) | protein | 311 | 6% helix, 49% strand | P14925 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, D
- NI · Nickel (II) ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · chains A, D
- FLC · Citrate anion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.77 | 0.82 | 96 | CU, FLC |
| 2 | 118 | 0.57 | 0.84 | 25 | GOL |
| 3 | 166 | 0.55 | 0.80 | 24 | empty |
| 4 | 122 | 0.55 | 0.82 | 23 | empty |
| 5 | 181 | 0.45 | 0.74 | 34 | GOL |
Interfaces
1 interface between chains.
- A–D · 930 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5WJA · Crystal structure of H107A 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 0.96
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 5WJA · PDBe 5WJA · UniProt P14925
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