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Ecorv restriction ENDONUCLEASE/GAAUTC/CA2+

Analyse Ecorv restriction ENDONUCLEASE/GAAUTC/CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B0E
Type: protein + DNA
Length: 491 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*AP*GP*AP*AP*(DU)P*TP*CP*TP*T)-3'; Type II restriction enzyme ecorv
EC: 3.1.21.4
UniProt: P04390
Ligands: CA
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-D(APAPAPGPAPAP(DU)PTPCPTP*T)-3'	dna	11	—	—
A	Type II restriction enzyme ecorv (EC 3.1.21.4)	protein	233	32% helix, 26% strand	P04390
B	Type II restriction enzyme ecorv (EC 3.1.21.4)	protein	236	34% helix, 30% strand	P04390

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, C

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	784	0.84	0.87	65	CA
2	241	0.55	0.78	37	empty
3	131	0.53	0.81	25	empty
4	162	0.47	0.77	19	empty
5	55	0.30	0.76	10	empty

Interfaces

6 interfaces between chains.

A–B · 1680 Å² buried · 19 hydrogen bonds · protein-protein
D–B · 720 Å² buried · 15 hydrogen bonds · protein-nucleic
C–A · 685 Å² buried · 14 hydrogen bonds · protein-nucleic
C–B · 520 Å² buried · 9 hydrogen bonds · protein-nucleic
C–D · 457 Å² buried · 38 hydrogen bonds · nucleic-nucleic

Compared structures

2B0E · EcoRV Restriction Endonuclease/GAAUTC/Ca2+ · the same entry in another collection · chain C against C, TM-score 1.00
P04390 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecorv (P04390) · a predicted model of the same protein · 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
Every structure of UniProt P04390
Elsewhere: RCSB PDB 2B0E · PDBe 2B0E · UniProt P04390

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