MolNFT v1 · #103484 · protein
Crystal structure of particulate methane monooxygenase from methylocystis sp. atcc 49242 (rockwell) soaked in zinc
4PI2 · Unknown peptide: “Crystal structure of particulate methane monooxygenase from methylocystis sp. atcc 49242 (rockwell) soaked in…”. X-ray diffraction, 2 ligands (ZN, CU), 20 pockets (best druggability 0.79). MolNFT v1 #103484 on…
- 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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