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Pi-scei, a homing endonuclease with protein splicing activity

Analyse Pi-scei, a homing endonuclease with protein splicing activity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VDE
Type: protein
Length: 857 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pi-scei
EC: 3.6.1.34
UniProt: P17255
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pi-scei (EC 3.6.1.34)	protein	429	26% helix, 35% strand	P17255
B	Pi-scei (EC 3.6.1.34)	protein	428	26% helix, 31% strand	P17255

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.75	0.80	79	empty
2	612	0.72	0.80	69	empty
3	289	0.53	0.75	37	empty
4	194	0.51	0.77	32	empty
5	119	0.51	0.80	18	empty

Interfaces

1 interface between chains.

A–B · 1424 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1VDE · Pi-scei, a homing endonuclease with protein splicing activity · the same entry in another collection · chain A against A, TM-score 1.00
P17255 · AlphaFold monomer V2.0 prediction for V-type proton ATPase catalytic subunit a (P17255) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P17255
Elsewhere: RCSB PDB 1VDE · PDBe 1VDE · UniProt P17255

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