Research workbench
Crystal structure of particulate methane monooxygenase from methylocystis sp. atcc 49242 (rockwell)
Analyse Crystal structure of particulate methane monooxygenase from methylocystis sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHZ
- Type
- protein
- Length
- 2,598 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unknown peptide; Particulate methane monooxygenase subunit C; Particulate methane…
- EC
- 1.14.18.3
- Ligands
- PGT, CU
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Unknown peptide | protein | 19 | 74% helix, 0% strand | — |
| H | Unknown peptide | protein | 20 | 70% helix, 0% strand | — |
| K | Particulate methane monooxygenase subunit C (EC 1.14.18.3) | protein | 213 | 75% helix, 1% strand | — |
| N | Unknown peptide | protein | 24 | 71% helix, 0% strand | — |
| A, E, I | Particulate methane monooxygenase subunit B (EC 1.14.18.3) | protein | 388 | 20% helix, 37% strand | — |
| B, F, J | Particulate methane monooxygenase subunit a (EC 1.14.18.3) | protein | 244 | 66% helix, 5% strand | — |
| C | Particulate methane monooxygenase subunit C (EC 1.14.18.3) | protein | 214 | 76% helix, 1% strand | — |
| G | Particulate methane monooxygenase subunit C (EC 1.14.18.3) | protein | 212 | 75% helix, 1% strand | — |
Ligands and binding sites
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 4 copies · chains K, N, D, C, H, G, F, J
- CU · Copper (II) ion · metal · 6 copies · chains K, A, E, I, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.81 | 0.82 | 102 | CU |
| 2 | 646 | 0.80 | 0.84 | 54 | PGT |
| 3 | 849 | 0.79 | 0.81 | 100 | CU |
| 4 | 645 | 0.78 | 0.83 | 49 | PGT |
| 5 | 1084 | 0.77 | 0.79 | 106 | PGT |
Interfaces
24 interfaces between chains.
- A–B · 3933 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 3904 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 3894 Ų buried · 26 hydrogen bonds · protein-protein
- K–J · 2823 Ų buried · 37 hydrogen bonds · protein-protein
- F–G · 2806 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4PHZ · Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242… · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4PHZ · PDBe 4PHZ
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