Research workbench

HPAD4 crystal complex with bb-F-amidine

Analyse HPAD4 crystal complex with bb-F-amidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N0M
Type: protein
Length: 636 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-arginine deiminase type-4
EC: 3.5.3.15
UniProt: Q9UM07
Ligands: 8HT, CA, SO4
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein-arginine deiminase type-4 (EC 3.5.3.15)	protein	636	22% helix, 37% strand	Q9UM07

Ligands and binding sites

8HT · ~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)-4-(2-fluoranylethanimidoylamino)butyl]-4-phenyl-benzamide · ligand · chains A
CA · Calcium ion · metal · 5 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	76	0.55	0.86	21	empty
2	101	0.42	0.78	18	SO4, 8HT
3	56	0.37	0.79	16	empty
4	85	0.36	0.76	15	empty

Modifications

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

Compared structures

5N0M · hPAD4 crystal complex with BB-F-amidine · the same entry in another collection · chain A against A, TM-score 1.00
Q9UM07 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-4 (Q9UM07) · 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 Q9UM07
Elsewhere: RCSB PDB 5N0M · PDBe 5N0M · UniProt Q9UM07

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