MolNFT v1 · #28460 · protein

Crystal structure of particulate methane monooxygenase

1YEW · Particulate methane monooxygenase, B subunit: “Crystal structure of particulate methane monooxygenase”. X-ray diffraction, 3 ligands (CUA, ZN, CU), 20 pockets (best druggability 0.77). MolNFT v1 #28460 on GenesisL1: 3D structure…

PDB: 1YEW
Type: protein
Length: 2,424 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Particulate methane monooxygenase, B subunit; Particulate methane monooxygenase, a…
UniProt: Q49104, Q607G3, O05111
Ligands: CUA, ZN, CU
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	Particulate methane monooxygenase, B subunit	protein	382	20% helix, 37% strand	Q49104
B, F, J	Particulate methane monooxygenase, a subunit	protein	238	60% helix, 3% strand	Q607G3
C, G, K	Particulate methane monooxygenase subunit C2	protein	188	69% helix, 0% strand	O05111

Ligands and binding sites

CUA · Dinuclear copper ion · ligand · 3 copies · chains A, E, I
ZN · Zinc ion · metal · 8 copies · chains A, B, C, E, F, G, J, K
CU · Copper (II) ion · metal · 3 copies · chains A, E, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	938	0.77	0.80	95	empty
2	697	0.77	0.82	92	empty
3	547	0.72	0.80	55	empty
4	957	0.72	0.76	116	empty
5	383	0.65	0.79	44	empty

Interfaces

21 interfaces between chains.

I–J · 3716 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 3711 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 3706 Å² buried · 40 hydrogen bonds · protein-protein
F–G · 3289 Å² buried · 26 hydrogen bonds · protein-protein
J–K · 3279 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

1YEW · Crystal structure of particulate methane monooxygenase · the same entry in another collection · chain K against K, TM-score 1.00
Q607G3 · AlphaFold monomer V2.0 prediction for particulate methane monooxygenase beta subunit… · a predicted model of the same protein · chain B against A, TM-score 0.79

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 Q49104
Every structure of UniProt Q607G3
Every structure of UniProt O05111
Elsewhere: RCSB PDB 1YEW · PDBe 1YEW · UniProt Q49104 · UniProt Q607G3 · UniProt O05111

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