Research workbench

Ecorv ENDONUCLEASE/DNA complex

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

PDB: 1AZ0
Type: protein + DNA
Length: 488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'); Protein (type II restriction enzyme…
EC: 3.1.21.4
UniProt: P04390
Ligands: CA
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'-D(APAPAPGPAPTPAPTPCPTP*T)-3')	dna	11	—	—
A	Protein (type II restriction enzyme ecorv) (EC 3.1.21.4)	protein	237	33% helix, 32% strand	P04390
B	Protein (type II restriction enzyme ecorv) (EC 3.1.21.4)	protein	229	31% helix, 31% strand	P04390

Ligands and binding sites

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

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	877	0.85	0.87	71	empty
2	173	0.57	0.81	25	empty
3	226	0.53	0.77	32	empty
4	66	0.40	0.80	12	empty
5	62	0.35	0.77	13	empty

Interfaces

6 interfaces between chains.

A–B · 1618 Å² buried · 20 hydrogen bonds · protein-protein
C–A · 718 Å² buried · 15 hydrogen bonds · protein-nucleic
D–B · 710 Å² buried · 14 hydrogen bonds · protein-nucleic
C–B · 492 Å² buried · 14 hydrogen bonds · protein-nucleic
C–D · 471 Å² buried · 41 hydrogen bonds · nucleic-nucleic

Compared structures

1AZ0 · Ecorv ENDONUCLEASE/DNA complex · 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 1AZ0 · PDBe 1AZ0 · UniProt P04390

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