MolNFT v1 · #114741 · protein

Crystal structure of unnamed thioesterase IPG2867 from legionella pneumophila

5BYU: “Crystal structure of unnamed thioesterase IPG2867 from legionella pneumophila”. X-ray diffraction, 1 ligand (COA), 14 pockets (best druggability 0.83). MolNFT v1 #114741 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5BYU
Type: protein
Length: 978 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioesterase
UniProt: Q5ZRL4
Ligands: COA
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 20% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H	Thioesterase	protein	128	20% helix, 46% strand	Q5ZRL4
C	Thioesterase	protein	123	20% helix, 45% strand	Q5ZRL4
D	Thioesterase	protein	103	20% helix, 47% strand	Q5ZRL4
E	Thioesterase	protein	122	20% helix, 47% strand	Q5ZRL4
F	Thioesterase	protein	119	17% helix, 47% strand	Q5ZRL4
G	Thioesterase	protein	127	20% helix, 46% strand	Q5ZRL4

Ligands and binding sites

COA · Coenzyme A · ligand · 4 copies · chains A, B, G, H

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

Pockets

14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	842	0.83	0.86	83	empty
2	899	0.83	0.85	96	empty
3	202	0.71	0.88	28	empty
4	223	0.71	0.86	31	empty
5	221	0.70	0.86	30	empty

Interfaces

13 interfaces between chains.

A–B · 890 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 887 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 823 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 818 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 596 Å² buried · 7 hydrogen bonds · protein-protein

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 Q5ZRL4
Elsewhere: RCSB PDB 5BYU · PDBe 5BYU · UniProt Q5ZRL4

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