Research workbench
Crystal structure of particulate methane monooxygenase from methylocystis sp. atcc 49242 (rockwell) soaked in zinc
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
- 4PI2
- Type
- protein
- Length
- 2,650 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unknown peptide; Particulate methane monooxygenase subunit a; Particulate methane…
- EC
- 1.14.18.3
- Ligands
- ZN, CU
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Unknown peptide | protein | 19 | 63% helix, 0% strand | — |
| H | Unknown peptide | protein | 20 | 75% helix, 0% strand | — |
| F, J, B | Particulate methane monooxygenase subunit a (EC 1.14.18.3) | protein | 244 | 65% helix, 3% strand | — |
| E, A, I | Particulate methane monooxygenase subunit B (EC 1.14.18.3) | protein | 390 | 19% helix, 36% strand | — |
| N | Unknown peptide | protein | 25 | 48% helix, 0% strand | — |
| G, K, C | Particulate methane monooxygenase subunit C (EC 1.14.18.3) | protein | 228 | 67% helix, 1% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains G, K, C
- CU · Copper (II) ion · metal · 3 copies · chains E, A, I
- CAC · Cacodylate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.79 | 0.82 | 69 | empty |
| 2 | 701 | 0.78 | 0.83 | 56 | empty |
| 3 | 643 | 0.78 | 0.83 | 44 | empty |
| 4 | 633 | 0.77 | 0.83 | 41 | empty |
| 5 | 624 | 0.76 | 0.82 | 43 | empty |
Interfaces
24 interfaces between chains.
- A–B · 3936 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 3920 Ų buried · 25 hydrogen bonds · protein-protein
- F–E · 3916 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 2970 Ų buried · 35 hydrogen bonds · protein-protein
- F–G · 2953 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4PI2 · 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 4PI2 · PDBe 4PI2
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