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Crystal structure of unbound beta-secretase catalytic domain.

Analyse Crystal structure of unbound beta-secretase catalytic domain. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SGZ
Type: protein
Length: 1,556 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase
EC: 3.4.23.46
UniProt: P56817
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-secretase (EC 3.4.23.46)	protein	389	17% helix, 39% strand	P56817

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.73	0.76	88	empty
2	465	0.70	0.81	53	empty
3	504	0.68	0.79	56	empty
4	546	0.66	0.77	49	empty
5	533	0.65	0.76	45	empty

Interfaces

4 interfaces between chains.

B–D · 555 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 454 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 306 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 126 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1SGZ · Crystal Structure of Unbound Beta-Secretase Catalytic Domain. · the same entry in another collection · chain B against B, TM-score 1.00
P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain D 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 P56817
Elsewhere: RCSB PDB 1SGZ · PDBe 1SGZ · UniProt P56817

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