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Complex structure of methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans

Analyse Complex structure of methane monooxygenase hydroxylase and regulatory subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M8R
Type: protein
Length: 2,416 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methane monooxygenase component a alpha chain; Methane monooxygenase beta chain; Methane…
UniProt: A0A2D2D5X0, A0A2D2D5X7, A0A2D2D0T0, A0A2D2D0T8
Ligands: BEZ, W6X, FE, CL
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 58% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Methane monooxygenase component a alpha chain	protein	515	61% helix, 4% strand	A0A2D2D5X0
B, F	Methane monooxygenase beta chain	protein	392	66% helix, 1% strand	A0A2D2D5X7
C, G	Methane monooxygenase gamma chain	protein	168	63% helix, 4% strand	A0A2D2D0T0
D	Methane monooxygenase regulatory protein B	protein	130	38% helix, 30% strand	A0A2D2D0T8
H	Methane monooxygenase regulatory protein B	protein	136	38% helix, 29% strand	A0A2D2D0T8

Ligands and binding sites

BEZ · Benzoic acid · ligand · 2 copies · chains A, E
W6X · 1,1,1-tris(fluoranyl)propan-2-one · ligand · 2 copies · chains D, H
FE · Fe (III) ion · metal · 4 copies · chains A, E
CL · Chloride ion · ion · chains D
EDO · 1,2-ethanediol · additive · 38 copies · chains A, D, B, C, H, F, E, G

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	826	0.86	0.89	69	EDO
2	155	0.82	0.97	35	EDO
3	142	0.82	0.98	35	EDO
4	108	0.79	0.98	26	empty
5	100	0.79	0.98	24	empty

Interfaces

18 interfaces between chains.

A–B · 5364 Å² buried · 86 hydrogen bonds · protein-protein
E–F · 5340 Å² buried · 91 hydrogen bonds · protein-protein
A–D · 2683 Å² buried · 38 hydrogen bonds · protein-protein
E–H · 2681 Å² buried · 38 hydrogen bonds · protein-protein
E–G · 2200 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

7M8R · Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with… · 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 7M8R · PDBe 7M8R · UniProt A0A2D2D5X0 · UniProt A0A2D2D5X7 · UniProt A0A2D2D0T0 · UniProt A0A2D2D0T8

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