MolNFT v1 · #93401 · protein

Cocrystal structure of glpg and dfp

4H1D · Rhomboid protease glpg: “Cocrystal structure of glpg and dfp”. X-ray diffraction, 1 ligand (DFP), 2 pockets (best druggability 0.47). MolNFT v1 #93401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4H1D
Type: protein
Length: 173 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhomboid protease glpg
EC: 3.4.21.105
UniProt: P09391
Ligands: DFP
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhomboid protease glpg (EC 3.4.21.105)	protein	173	76% helix, 0% strand	P09391

Ligands and binding sites

DFP · Diisopropyl phosphonate · ligand · chains A

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

Pockets

2 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	133	0.47	0.78	26	DFP
2	64	0.34	0.76	16	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4H1D · Cocrystal structure of GlpG and DFP · the same entry in another collection · chain A against A, TM-score 1.00
P09391 · AlphaFold monomer V2.0 prediction for rhomboid protease glpg (P09391) · a predicted model of the same protein · chain A 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 P09391
Elsewhere: RCSB PDB 4H1D · PDBe 4H1D · UniProt P09391

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