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Secreted aspartic protease 1 from candida parapsilosis in complex with pepstatin a

Analyse Secreted aspartic protease 1 from candida parapsilosis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FV3
Type: protein
Length: 2,751 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SAPP1P-secreted aspartic protease 1; Pepstatin a
EC: 3.4.23.24
Ligands: IVA, SO4
Pockets: 20 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F, G, H	SAPP1P-secreted aspartic protease 1 (EC 3.4.23.24)	protein	339	9% helix, 50% strand	—
I, J, K, L, M, N, O, P	Pepstatin a	protein	5	0% helix, 20% strand	—
D	SAPP1P-secreted aspartic protease 1 (EC 3.4.23.24)	protein	338	9% helix, 48% strand	—

Ligands and binding sites

IVA · Isovaleric acid · ligand · 8 copies · chains A, I, B, J, C, K, D, L, E, M, F, N, G, O, H, P
SO4 · Sulfate ion · ion · 15 copies · chains B, D, E, F, G, O, H, A
GOL · Glycerol · additive · 25 copies · chains B, J, C, K, D, L, E, M, F, G, H, P, A, I

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

Pockets

20 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.50	0.73	39	GOL
2	119	0.42	0.77	16	empty
3	120	0.41	0.76	15	empty
4	134	0.41	0.75	23	empty
5	69	0.40	0.80	20	empty

Interfaces

12 interfaces between chains.

E–M · 594 Å² buried · 14 hydrogen bonds · protein-protein
G–O · 584 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 584 Å² buried · 14 hydrogen bonds · protein-protein
C–K · 566 Å² buried · 13 hydrogen bonds · protein-protein
A–I · 565 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 16 modified, 8 covalent (disulfide, nonstandard, covalent ligand).

Compared structures

3FV3 · Secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A · 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
Elsewhere: RCSB PDB 3FV3 · PDBe 3FV3

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