MolNFT v1 · #119750 · protein

Structure of the pyrococcus furiosus esterase PF2001 with space group P21

5G5M: “Structure of the pyrococcus furiosus esterase PF2001 with space group P21”. X-ray diffraction, 1 ligand (QRL), 3 pockets (best druggability 0.72). MolNFT v1 #119750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5G5M
Type: protein
Length: 510 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esterase
UniProt: Q8TZJ1
Ligands: QRL
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Esterase	protein	253	40% helix, 20% strand	Q8TZJ1
B	Esterase	protein	257	40% helix, 19% strand	Q8TZJ1

Ligands and binding sites

QRL · S-methyl hexanethioate · ligand · 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	420	0.72	0.83	41	QRL
2	137	0.50	0.78	19	empty
3	116	0.44	0.77	24	empty

Interfaces

1 interface between chains.

A–B · 1129 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5G5M · Structure of the Pyrococcus Furiosus Esterase Pf2001 with space group P21 · 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 Q8TZJ1
Elsewhere: RCSB PDB 5G5M · PDBe 5G5M · UniProt Q8TZJ1

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