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The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA fragments

Analyse The crystal structure of ecorv endonuclease and of its complexes with cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RVE
Type: protein
Length: 488 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease ecor V
EC: 3.1.21.4
UniProt: P04390
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Endonuclease ecor V (EC 3.1.21.4)	protein	244	31% helix, 28% strand	P04390

Pockets

4 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	788	0.71	0.77	90	empty
2	136	0.54	0.82	21	empty
3	74	0.51	0.84	16	empty
4	109	0.40	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 1568 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1RVE · The crystal structure of ecorv endonuclease and of its complexes with cognate and… · the same entry in another collection · chain A against A, 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 0.93

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 1RVE · PDBe 1RVE · UniProt P04390

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