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Crystal structure of a putative endoribonuclease L-psp from entamoeba histolytica, orthorhombic form

Analyse Crystal structure of a putative endoribonuclease L-psp from entamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M4S
Type: protein
Length: 751 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative endoribonuclease L-psp
UniProt: C4LXT9
Ligands: CL
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Putative endoribonuclease L-psp	protein	125	31% helix, 35% strand	C4LXT9
F	Putative endoribonuclease L-psp	protein	126	31% helix, 35% strand	C4LXT9

Ligands and binding sites

CL · Chloride ion · ion · chains B

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

Pockets

9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	122	0.81	0.99	31	empty
2	113	0.81	0.99	31	empty
3	878	0.72	0.77	77	empty
4	117	0.59	0.85	18	empty
5	108	0.57	0.85	20	empty

Interfaces

9 interfaces between chains.

A–C · 939 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 915 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 909 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 902 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 891 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3M4S · Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica… · the same entry in another collection · 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 C4LXT9
Elsewhere: RCSB PDB 3M4S · PDBe 3M4S · UniProt C4LXT9

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