MolNFT v1 · #175905 · protein
BACE2 xaperone complex with N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxo- 5,6-dihydro-2H-1LAMBDA6,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5- fluoropyridine-2-carboxamide
7D5B · Beta-secretase 2: “BACE2 xaperone complex with N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxo…”. X-ray diffraction, 3 ligands (66F, NA, CL), 4 pockets (best druggability 0.65). MolNFT v1 #175905 on GenesisL1: 3D structure, binding sites…
- PDB
- 7D5B
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 2; Xaperone
- EC
- 3.4.23.45
- UniProt
- Q9Y5Z0
- Ligands
- 66F, NA, CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 2 (EC 3.4.23.45) | protein | 369 | 15% helix, 41% strand | Q9Y5Z0 |
| D | Xaperone | protein | 112 | 11% helix, 51% strand | — |
Ligands and binding sites
- 66F · N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, D
- CL · Chloride ion · ion · chains A, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.65 | 0.78 | 45 | 66F, EDO |
| 2 | 116 | 0.40 | 0.76 | 23 | empty |
| 3 | 72 | 0.32 | 0.75 | 16 | empty |
| 4 | 52 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 869 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7D5B · BACE2 xaperone complex with N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxo-5,6-dihydro-2H-1lamb… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5Z0 · AlphaFold monomer V2.0 prediction for beta-secretase 2 (Q9Y5Z0) · 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 Q9Y5Z0
- Elsewhere: RCSB PDB 7D5B · PDBe 7D5B · UniProt Q9Y5Z0
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