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Crystal structure of human beta-secretase in complex with nvp-BAV544

Analyse Crystal structure of human beta-secretase in complex with nvp-BAV544 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DV5
Type: protein
Length: 1,135 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1
EC: 3.4.23.46
UniProt: P56817
Ligands: BAV
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 1 (EC 3.4.23.46)	protein	377	16% helix, 41% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	381	17% helix, 40% strand	P56817

Ligands and binding sites

BAV · (3S,14R,16S)-16-[(1R)-1-hydroxy-2-{[3-(1-methylethyl) benzyl]amino}ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5- dione · ligand · 3 copies · chains A, B, C

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.81	0.83	127	BAV
2	564	0.72	0.80	65	BAV
3	174	0.58	0.82	36	empty
4	111	0.43	0.77	21	empty
5	149	0.43	0.75	20	empty

Interfaces

2 interfaces between chains.

A–C · 1056 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 584 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3DV5 · Crystal structure of human beta-secretase in complex with NVP-BAV544 · the same entry in another collection · chain A against A, TM-score 1.00
P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 3DV5 · PDBe 3DV5 · UniProt P56817

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