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Crystal structure of intein homing endonuclease II

Analyse Crystal structure of intein homing endonuclease II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CW7
Type: protein
Length: 537 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease pi-pkoii
EC: 3.1.-.-
UniProt: P77933
Ligands: SO4
Pockets: 4 · best druggability 0.37

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endonuclease pi-pkoii (EC 3.1.-.-)	protein	537	32% helix, 31% strand	P77933

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.37	0.78	14	empty
2	104	0.34	0.73	21	empty
3	61	0.32	0.76	15	empty
4	72	0.31	0.74	17	empty

Compared structures

2CW7 · Crystal structure of intein homing endonuclease II · the same entry in another collection · chain A against A, TM-score 1.00
P77933 · AlphaFold monomer V2.0 prediction for DNA polymerase (P77933) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P77933
Elsewhere: RCSB PDB 2CW7 · PDBe 2CW7 · UniProt P77933

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