MolNFT v1 · #31605 · protein + DNA

Ecorv restriction ENDONUCLEASE/GAATTC/CA2+

2B0D · 5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3': “Ecorv restriction ENDONUCLEASE/GAATTC/CA2+”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.83). MolNFT v1 #31605 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2B0D
Type: protein + DNA
Length: 497 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*AP*GP*AP*AP*TP*TP*CP*TP*T)-3'; Type II restriction enzyme ecorv
EC: 3.1.21.4
UniProt: P04390
Ligands: CA
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-D(APAPAPGPAPAPTPTPCPTP*T)-3'	dna	11	—	—
A	Type II restriction enzyme ecorv (EC 3.1.21.4)	protein	236	31% helix, 28% strand	P04390
B	Type II restriction enzyme ecorv (EC 3.1.21.4)	protein	239	31% helix, 28% 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

3 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	900	0.83	0.86	70	CA
2	452	0.64	0.78	54	empty
3	227	0.57	0.79	28	empty

Interfaces

6 interfaces between chains.

A–B · 1697 Å² buried · 25 hydrogen bonds · protein-protein
D–B · 699 Å² buried · 16 hydrogen bonds · protein-nucleic
C–A · 665 Å² buried · 17 hydrogen bonds · protein-nucleic
C–B · 476 Å² buried · 13 hydrogen bonds · protein-nucleic
C–D · 469 Å² buried · 45 hydrogen bonds · nucleic-nucleic

Compared structures

2B0D · EcoRV Restriction Endonuclease/GAATTC/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 2B0D · PDBe 2B0D · UniProt P04390

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