MolNFT v1 · #75485 · protein

Alpha-lytic protease complexed with C-terminal truncated pro region

3PRO: “Alpha-lytic protease complexed with C-terminal truncated pro region”. X-ray diffraction, 1 ligand (AES), 7 pockets (best druggability 0.61). MolNFT v1 #75485 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PRO
Type: protein
Length: 698 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-lytic protease
UniProt: P00778
Ligands: AES
Pockets: 7 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-lytic protease	protein	198	7% helix, 56% strand	P00778
C	Alpha-lytic protease	protein	150	45% helix, 27% strand	P00778
D	Alpha-lytic protease	protein	152	44% helix, 27% strand	P00778

Ligands and binding sites

AES · 4-(2-aminoethyl)benzenesulfonyl fluoride · ligand · 2 copies · chains A, C, B, D

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	387	0.61	0.77	45	empty
2	364	0.59	0.76	48	empty
3	209	0.51	0.77	28	empty
4	211	0.50	0.76	28	empty
5	146	0.44	0.76	19	AES

Interfaces

4 interfaces between chains.

A–C · 1359 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1210 Å² buried · 14 hydrogen bonds · protein-protein
C–B · 227 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 26 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

3PRO · Alpha-lytic protease complexed with C-terminal truncated pro region · the same entry in another collection · chain B against B, TM-score 1.00
P00778 · AlphaFold monomer V2.0 prediction for alpha-lytic protease (P00778) · a predicted model of the same protein · 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 P00778
Elsewhere: RCSB PDB 3PRO · PDBe 3PRO · UniProt P00778

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.