MolNFT v1 · #106557 · protein

Crystal structure of X-prolyl aminopeptidase from caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

4S2T · Protein app-1: “Crystal structure of X-prolyl aminopeptidase from caenorhabditis elegans: a cytosolic enzyme with a…”. X-ray diffraction, 3 ligands (01B, ZN, SO4), 16 pockets (best druggability 0.78). MolNFT v1 #106557 on GenesisL1…

PDB: 4S2T
Type: protein
Length: 1,233 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein app-1; Apstatin
UniProt: O44750
Ligands: 01B, ZN, SO4
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Protein app-1	protein	615	41% helix, 21% strand	O44750
Q	Protein app-1	protein	612	42% helix, 20% strand	O44750
A, B	Apstatin	protein	3	0% helix, 0% strand	—

Ligands and binding sites

01B · (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid · ligand · 2 copies · chains P, A, Q, B
ZN · Zinc ion · metal · 4 copies · chains P, A, Q, B
SO4 · Sulfate ion · ion · 7 copies · chains P, Q

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1170	0.78	0.80	98	empty
2	590	0.70	0.78	61	empty
3	422	0.69	0.81	41	empty
4	475	0.66	0.78	46	SO4
5	346	0.62	0.78	38	empty

Interfaces

3 interfaces between chains.

P–Q · 2037 Å² buried · 14 hydrogen bonds · protein-protein
P–A · 305 Å² buried · 4 hydrogen bonds · protein-protein
Q–B · 281 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4S2T · Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic… · the same entry in another collection · chain P against P, TM-score 1.00
O44750 · AlphaFold monomer V2.0 prediction for xaa-pro aminopeptidase app-1 (O44750) · a predicted model of the same protein · chain Q against A, TM-score 0.98

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 O44750
Elsewhere: RCSB PDB 4S2T · PDBe 4S2T · UniProt O44750

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