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Q138F hincii bound to cognate DNA gttaac

Analyse Q138F hincii bound to cognate DNA gttaac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GII
Type: protein + DNA
Length: 493 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3'; Type II restriction enzyme hincii
EC: 3.1.21.4
UniProt: P44413
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F	5'-D(GPCPCPGPGPTPTPAPAPCPCPGPGPC)-3'	dna	14	—	—
A	Type II restriction enzyme hincii (EC 3.1.21.4)	protein	238	41% helix, 20% strand	P44413
B	Type II restriction enzyme hincii (EC 3.1.21.4)	protein	227	41% helix, 18% strand	P44413

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	577	0.72	0.80	49	empty
2	539	0.69	0.79	39	empty
3	149	0.47	0.77	20	empty
4	135	0.47	0.77	17	empty
5	183	0.46	0.75	21	empty

Interfaces

6 interfaces between chains.

A–B · 1208 Å² buried · 6 hydrogen bonds · protein-protein
E–B · 796 Å² buried · 10 hydrogen bonds · protein-nucleic
F–A · 767 Å² buried · 11 hydrogen bonds · protein-nucleic
E–F · 629 Å² buried · 52 hydrogen bonds · nucleic-nucleic
F–B · 507 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

2GII · Q138F HincII bound to cognate DNA GTTAAC · the same entry in another collection · chain E against E, TM-score 1.00
P44413 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme hindii (P44413) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P44413
Elsewhere: RCSB PDB 2GII · PDBe 2GII · UniProt P44413

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