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Crystal structure of L. monocytogenes phosphodiesterase pgph hd domain

Analyse Crystal structure of L. monocytogenes phosphodiesterase pgph hd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S1C
Type: protein
Length: 416 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LMO1466 protein
UniProt: Q8Y746
Ligands: FE
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	LMO1466 protein	protein	208	70% helix, 1% strand	Q8Y746
A	LMO1466 protein	protein	208	70% helix, 1% strand	Q8Y746

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains D, A

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

Pockets

5 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	396	0.69	0.81	37	empty
2	358	0.68	0.82	34	empty
3	211	0.58	0.80	32	empty
4	57	0.30	0.75	16	empty
5	57	0.26	0.72	13	empty

Interfaces

1 interface between chains.

D–A · 606 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4S1C · Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain · the same entry in another collection · chain D against D, 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 Q8Y746
Elsewhere: RCSB PDB 4S1C · PDBe 4S1C · UniProt Q8Y746

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