MolNFT v1 · #171929 · protein

Crystal structure of C173S mutation in the PMGL2 esterase from permafrost metagenomic library

6ZL7: “Crystal structure of C173S mutation in the PMGL2 esterase from permafrost metagenomic library”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.78). MolNFT v1 #171929 on GenesisL1: 3D structure, binding sites and…

PDB: 6ZL7
Type: protein
Length: 636 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
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PMGL2 (EC 3.1.1.3)	protein	317	41% helix, 15% strand	A0A142J6I6
B	PMGL2 (EC 3.1.1.3)	protein	319	42% helix, 15% strand	A0A142J6I6

Ligands and binding sites

MG · Magnesium ion · metal · chains A, B
PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	721	0.78	0.82	85	PG6
2	680	0.72	0.78	61	PG6
3	135	0.42	0.76	32	MG
4	79	0.37	0.76	17	empty
5	73	0.34	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1573 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6ZL7 · Crystal structure of C173S mutation in the PMGL2 esterase 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 6ZL7 · PDBe 6ZL7 · UniProt A0A142J6I6

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