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Crystal structure of methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase and regulatory component complex

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

PDB: 6VK4
Type: protein
Length: 2,406 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methane monooxygenase component a alpha chain; Methane monooxygenase; Methane…
UniProt: A0A2D2D5X0, A0A2D2D5X7, A0A2D2D0T0, A0A2D2D0T8
Ligands: BEZ, FE, FE2
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Methane monooxygenase component a alpha chain	protein	515	60% helix, 4% strand	A0A2D2D5X0
B, F	Methane monooxygenase	protein	391	66% helix, 1% strand	A0A2D2D5X7
C, G	Methane monooxygenase	protein	167	63% helix, 4% strand	A0A2D2D0T0
D, H	Methane monooxygenase regulatory protein B	protein	130	37% helix, 30% strand	A0A2D2D0T8

Ligands and binding sites

BEZ · Benzoic acid · ligand · 2 copies · chains A, E
FE · Fe (III) ion · metal · 2 copies · chains A
FE2 · Fe (II) ion · metal · 2 copies · chains E
EDO · 1,2-ethanediol · additive · chains A, 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	963	0.87	0.88	110	empty
2	114	0.81	0.99	37	empty
3	112	0.79	0.98	33	empty
4	104	0.79	0.99	25	empty
5	78	0.77	0.99	25	BEZ

Interfaces

18 interfaces between chains.

A–B · 5407 Å² buried · 89 hydrogen bonds · protein-protein
E–F · 5352 Å² buried · 91 hydrogen bonds · protein-protein
E–H · 2718 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 2686 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 2247 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

6VK4 · Crystal Structure of Methylosinus trichosporium OB3b Soluble 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 A0A2D2D5X0
Every structure of UniProt A0A2D2D5X7
Every structure of UniProt A0A2D2D0T0
Every structure of UniProt A0A2D2D0T8
Elsewhere: RCSB PDB 6VK4 · PDBe 6VK4 · UniProt A0A2D2D5X0 · UniProt A0A2D2D5X7 · UniProt A0A2D2D0T0 · UniProt A0A2D2D0T8

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