MolNFT v1 · #120028 · protein

Crystal structure of a family VIII carboxylesterase

5GMX: “Crystal structure of a family VIII carboxylesterase”. X-ray diffraction, 1 ligand (PMS), 3 pockets (best druggability 0.62). MolNFT v1 #120028 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GMX
Type: protein
Length: 738 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carboxylesterase
EC: 3.1.1.1
UniProt: A0A0G2RKR9
Ligands: PMS
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Carboxylesterase (EC 3.1.1.1)	protein	369	36% helix, 18% strand	A0A0G2RKR9

Ligands and binding sites

PMS · phenylmethanesulfonic acid · ligand · 2 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	519	0.62	0.75	51	empty
2	134	0.56	0.82	24	PMS
3	125	0.56	0.83	23	PMS

Interfaces

1 interface between chains.

A–B · 169 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 22 modified, 2 covalent (engineered, covalent ligand).

Compared structures

5GMX · Crystal structure of a family VIII carboxylesterase · 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 A0A0G2RKR9
Elsewhere: RCSB PDB 5GMX · PDBe 5GMX · UniProt A0A0G2RKR9

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