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Crystal structure of methylosinus trichosporium OB3B particulate methane monooxygenase (pmmo)

Analyse Crystal structure of methylosinus trichosporium OB3B particulate methane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CHX
Type: protein
Length: 2,415 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pmob; Pmoa; Pmoc; 20-residue peptide; 26-residue peptide
UniProt: Q9KX50, Q50541, Q9KX51
Ligands: CU
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 38% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	Pmob	protein	362	13% helix, 23% strand	Q9KX50
B, F, J	Pmoa	protein	238	51% helix, 3% strand	Q50541
C, G, K	Pmoc	protein	159	60% helix, 0% strand	Q9KX51
D, H, L	20-residue peptide	protein	20	75% helix, 0% strand	—
M, N, O	26-residue peptide	protein	26	92% helix, 0% strand	—

Ligands and binding sites

CU · Copper (II) ion · metal · 9 copies · chains B, C, A, F, G, E, J, K, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	886	0.80	0.82	100	empty
2	545	0.80	0.85	44	empty
3	813	0.79	0.82	85	empty
4	553	0.79	0.85	44	empty
5	554	0.77	0.83	45	empty

Interfaces

33 interfaces between chains.

I–J · 3537 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 3533 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 3524 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 2264 Å² buried · 28 hydrogen bonds · protein-protein
J–K · 2262 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

3CHX · Crystal structure of Methylosinus trichosporium OB3b particulate methane monooxygenase… · the same entry in another collection · chain A against A, 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
Every structure of UniProt Q9KX50
Every structure of UniProt Q50541
Every structure of UniProt Q9KX51
Elsewhere: RCSB PDB 3CHX · PDBe 3CHX · UniProt Q9KX50 · UniProt Q50541 · UniProt Q9KX51

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