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Protease SAPP1P from candida parapsilosis in complex with KB74

Analyse Protease SAPP1P from candida parapsilosis in complex with KB74 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AGC
Type: protein
Length: 1,372 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Candidapepsin; KB74
EC: 3.4.23.24
UniProt: B8YPM3
Ligands: BOC, FOR
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F	Candidapepsin (EC 3.4.23.24)	protein	339	9% helix, 50% strand	B8YPM3
E, I, C, G	KB74	protein	4	0% helix, 25% strand	—

Ligands and binding sites

BOC · Tert-butyl hydrogen carbonate · ligand · 4 copies · chains D, E, A, I, B, C, F, G
FOR · Formyl group · ligand · 4 copies · chains D, E, A, I, B, C, F, G
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, I, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
PGE · Triethylene glycol · additive · chains A, I

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	932	0.82	0.84	84	FOR
2	811	0.71	0.77	78	empty
3	216	0.66	0.85	47	MES
4	460	0.59	0.74	63	BOC, PGE
5	233	0.56	0.78	39	PEG, FOR

Interfaces

9 interfaces between chains.

A–B · 1179 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 538 Å² buried · 12 hydrogen bonds · protein-protein
F–G · 479 Å² buried · 14 hydrogen bonds · protein-protein
A–I · 477 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 475 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 7 covalent, 4 modified (disulfide, covalent ligand, nonstandard).

Compared structures

7AGC · Protease Sapp1p from Candida parapsilosis in complex with KB74 · 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
Every structure of UniProt B8YPM3
Elsewhere: RCSB PDB 7AGC · PDBe 7AGC · UniProt B8YPM3

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