Research workbench

Q138F hincii bound to gtcgac and 5 mm CA2+

Analyse Q138F hincii bound to gtcgac and 5 mm CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3E41
Type: protein + DNA
Length: 517 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type-2 restriction enzyme hindii; 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DG…
EC: 3.1.21.4
UniProt: P44413
Ligands: CA, NA
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type-2 restriction enzyme hindii (EC 3.1.21.4)	protein	246	41% helix, 22% strand	P44413
B	Type-2 restriction enzyme hindii (EC 3.1.21.4)	protein	243	42% helix, 20% strand	P44413
E, F	5'-D(DGPDCPDCPDGPDGPDTPDCPDGPDAPDCPDCPDGPDGPD C)-3'	dna	14	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, F, B, E
NA · Sodium ion · metal · chains B, E

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.73	0.77	79	CA
2	415	0.71	0.82	30	empty
3	230	0.52	0.76	29	empty
4	144	0.43	0.75	18	empty
5	63	0.33	0.77	13	empty

Interfaces

6 interfaces between chains.

A–B · 1219 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 879 Å² buried · 24 hydrogen bonds · protein-nucleic
B–E · 876 Å² buried · 19 hydrogen bonds · protein-nucleic
E–F · 658 Å² buried · 64 hydrogen bonds · nucleic-nucleic
A–E · 541 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

3E41 · Q138F HincII bound to GTCGAC and 5 mM Ca2+ · the same entry in another collection · chain A against A, 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 B 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 3E41 · PDBe 3E41 · UniProt P44413

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.