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Notum fragment 823

Analyse Notum fragment 823 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BD3
Type: protein
Length: 355 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: TE5, NAG, SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98)	protein	355	33% helix, 18% strand	Q6P988

Ligands and binding sites

TE5 · 4-methoxy-6-phenyl-pyrimidin-2-amine · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A

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

Pockets

4 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	137	0.71	0.91	24	TE5
2	137	0.47	0.77	19	empty
3	81	0.36	0.76	17	empty
4	52	0.31	0.76	10	empty

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7BD3 · Notum Fragment 823 · 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 7BD3 · PDBe 7BD3 · UniProt Q6P988

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