MolNFT v1 · #28315 · protein

Crystal structure of human liver carboxylesterase in complex with benzil

1YAJ · CES1 protein: “Crystal structure of human liver carboxylesterase in complex with benzil”. X-ray diffraction, 4 ligands (BEZ, NAG, SIA), 20 pockets (best druggability 0.81). MolNFT v1 #28315 on GenesisL1: 3D structure, binding sites…

PDB: 1YAJ
Type: protein
Length: 6,384 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CES1 protein
EC: 3.1.1.1
UniProt: P23141
Ligands: BEZ, NAG, SIA, SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	CES1 protein (EC 3.1.1.1)	protein	532	36% helix, 17% strand	P23141

Ligands and binding sites

BEZ · Benzoic acid · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
SIA · N-acetyl-alpha-neuraminic acid · sugar · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
SO4 · Sulfate ion · ion · 24 copies · chains A, C, B, D, F, E, G, I, H, J, L, K

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.81	0.90	47	BEZ
2	373	0.81	0.90	47	BEZ
3	1049	0.81	0.82	142	SIA, SO4
4	338	0.81	0.91	53	BEZ
5	366	0.80	0.89	46	BEZ

Interfaces

17 interfaces between chains.

A–B · 646 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 606 Å² buried · 6 hydrogen bonds · protein-protein
K–L · 604 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 598 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 588 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 12 glycan, 3 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

1YAJ · Crystal Structure of Human Liver Carboxylesterase in complex with benzil · the same entry in another collection · chain L against L, 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 P23141
Elsewhere: RCSB PDB 1YAJ · PDBe 1YAJ · UniProt P23141

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