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Crystal structure of the PMGL2 esterase (point mutant 1) from permafrost metagenomic library

Analyse Crystal structure of the PMGL2 esterase (point mutant 1) from permafrost… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QLA
Type: protein
Length: 638 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PMGL2
EC: 3.1.1.3
UniProt: A0A142J6I6
Ligands: MG, CL
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	PMGL2 (EC 3.1.1.3)	protein	319	42% helix, 15% strand	A0A142J6I6

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B
CL · Chloride ion · ion · chains A, B
PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.78	0.96	29	empty
2	642	0.72	0.79	58	PG6
3	668	0.71	0.78	61	PG6
4	129	0.41	0.76	33	CL, MG
5	71	0.34	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1666 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6QLA · CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE (point mutant 1) FROM PERMAFROST METAGENOMIC… · 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 A0A142J6I6
Elsewhere: RCSB PDB 6QLA · PDBe 6QLA · UniProt A0A142J6I6

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