MolNFT v1 · #172032 · protein

Enteropeptidase in complex with compound 6

6ZOV: “Enteropeptidase in complex with compound 6”. X-ray diffraction, 1 ligand (GBS), 11 pockets (best druggability 0.78). MolNFT v1 #172032 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZOV
Type: protein
Length: 938 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enteropeptidase
EC: 3.4.21.9
UniProt: P98073
Ligands: GBS
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Enteropeptidase (EC 3.4.21.9)	protein	234	9% helix, 37% strand	P98073
B, D	Enteropeptidase (EC 3.4.21.9)	protein	235	8% helix, 37% strand	P98073

Ligands and binding sites

GBS · 4-guanidinobenzoic acid · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 6 copies · chains B, D
PGE · Triethylene glycol · additive · chains A, B
GOL · Glycerol · additive · chains B, D

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.78	0.83	92	EDO, GOL
2	100	0.64	0.89	19	empty
3	192	0.49	0.76	36	GBS
4	149	0.46	0.77	32	GBS
5	57	0.46	0.84	13	empty

Interfaces

5 interfaces between chains.

A–D · 727 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 707 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 453 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 413 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 112 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

6ZOV · Enteropeptidase in complex with compound 6 · the same entry in another collection · chain D against D, TM-score 1.00
P98073 · AlphaFold monomer V2.0 prediction for enteropeptidase (P98073) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P98073
Elsewhere: RCSB PDB 6ZOV · PDBe 6ZOV · UniProt P98073

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