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Crystal structure of a type II restriction endonuclease

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

PDB: 4L0K
Type: protein
Length: 821 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Draiii
Pockets: 8 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Draiii	protein	208	45% helix, 11% strand	—
B	Draiii	protein	202	48% helix, 11% strand	—
C	Draiii	protein	204	46% helix, 11% strand	—
D	Draiii	protein	207	50% helix, 11% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.56	0.75	36	empty
2	239	0.55	0.77	34	empty
3	222	0.51	0.76	28	empty
4	250	0.50	0.75	26	empty
5	193	0.48	0.76	24	empty

Interfaces

4 interfaces between chains.

A–C · 976 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 963 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 424 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 100 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

4L0K · Crystal structure of a type II restriction endonuclease · 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
Elsewhere: RCSB PDB 4L0K · PDBe 4L0K

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