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Crystal structure of human beta secretase complexed with nvp-AMK640

Analyse Crystal structure of human beta secretase complexed with nvp-AMK640 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YM4
Type: protein
Length: 1,147 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1; Nvp-AMK640 inhibitor
EC: 3.4.23.46
UniProt: P56817
Ligands: 24M
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Beta-secretase 1 (EC 3.4.23.46)	protein	379	13% helix, 40% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	377	16% helix, 41% strand	P56817
X, Y, Z	Nvp-AMK640 inhibitor	protein	4	0% helix, 0% strand	—

Ligands and binding sites

24M · (1R,2R)-2-[(1S,2S)-2-amino-1-hydroxy-4-methylpentyl]cyclopentanecarboxylic acid · ligand · 3 copies · chains A, X, B, Y, C, Z

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.72	0.76	84	24M
2	118	0.71	0.92	26	24M
3	105	0.71	0.93	29	24M
4	84	0.66	0.92	20	empty
5	121	0.61	0.86	35	empty

Interfaces

5 interfaces between chains.

A–C · 772 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 590 Å² buried · 12 hydrogen bonds · protein-protein
A–X · 555 Å² buried · 14 hydrogen bonds · protein-protein
C–Z · 541 Å² buried · 11 hydrogen bonds · protein-protein
B–Y · 538 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 6 covalent (disulfide, covalent ligand).

Compared structures

1YM4 · Crystal structure of human beta secretase complexed with NVP-AMK640 · the same entry in another collection · chain Z against Z, 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 1YM4 · PDBe 1YM4 · UniProt P56817

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