MolNFT v1 · #173864 · protein

Notum fragment 916

7BDB · Palmitoleoyl-protein carboxylesterase notum: “Notum fragment 916”. X-ray diffraction, 3 ligands (NW7, NAG, SO4), 2 pockets (best druggability 0.70). MolNFT v1 #173864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7BDB
Type: protein
Length: 341 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Palmitoleoyl-protein carboxylesterase notum
EC: 3.1.1.98
UniProt: Q6P988
Ligands: NW7, NAG, SO4
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98)	protein	341	34% helix, 18% strand	Q6P988

Ligands and binding sites

NW7 · 3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

2 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	156	0.70	0.89	20	NW7
2	64	0.30	0.74	21	empty

Modifications

Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7BDB · Notum Fragment 916 · 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 Q6P988
Elsewhere: RCSB PDB 7BDB · PDBe 7BDB · UniProt Q6P988

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