MolNFT v1 · #119969 · protein

The crystal structure of nattokinase fragments

5GL8 · Subtilisin nat: “The crystal structure of nattokinase fragments”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.43). MolNFT v1 #119969 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GL8
Type: protein
Length: 550 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Subtilisin nat
EC: 3.4.21.62
UniProt: P35835
Ligands: CA
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Subtilisin nat (EC 3.4.21.62)	protein	275	30% helix, 20% strand	P35835

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains B

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

Pockets

3 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	206	0.43	0.73	29	empty
2	97	0.36	0.75	29	empty
3	80	0.34	0.75	24	empty

Interfaces

1 interface between chains.

A–B · 53 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5GL8 · The crystal structure of Nattokinase fragments · the same entry in another collection · chain A against A, TM-score 1.00
P35835 · AlphaFold monomer V2.0 prediction for subtilisin nat (P35835) · 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 P35835
Elsewhere: RCSB PDB 5GL8 · PDBe 5GL8 · UniProt P35835

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