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Crystal structure of mgs-M1, an ALPHA/BETA hydrolase enzyme from a medee basin deep-sea metagenome library

Analyse Crystal structure of mgs-M1, an ALPHA/BETA hydrolase enzyme from a medee basin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q3K
Type: protein
Length: 483 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mgs-M1
Ligands: CL, F
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mgs-M1	protein	241	31% helix, 22% strand	—
B	Mgs-M1	protein	242	34% helix, 22% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B
F · Fluoride ion · ion · 2 copies · chains A, B
PGE · Triethylene glycol · additive · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.70	0.78	54	empty
2	113	0.39	0.75	24	PGE
3	109	0.37	0.74	23	F, PGE

Interfaces

1 interface between chains.

A–B · 1543 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4Q3K · Crystal structure of MGS-M1, an alpha/beta hydrolase enzyme from a Medee basin deep-sea… · the same entry in another collection · chain B against B, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4Q3K · PDBe 4Q3K

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