Research workbench

Ecorv bound to cognate DNA

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

PDB: 1EOP
Type: protein + DNA
Length: 501 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*C)- 3'); Type II restriction enzyme ecorv
EC: 3.1.21.4
UniProt: P04390
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'-D(GPAPAPGPAPTPAPTPCPTPTPC)- 3')	dna	11	—	—
A	Type II restriction enzyme ecorv (EC 3.1.21.4)	protein	238	33% helix, 25% strand	P04390
B	Type II restriction enzyme ecorv (EC 3.1.21.4)	protein	241	32% helix, 26% strand	P04390

Pockets

7 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	496	0.84	0.91	66	empty
2	246	0.54	0.77	36	empty
3	138	0.52	0.80	25	empty
4	92	0.37	0.75	17	empty
5	72	0.36	0.77	13	empty

Interfaces

6 interfaces between chains.

A–B · 1934 Å² buried · 18 hydrogen bonds · protein-protein
C–A · 808 Å² buried · 15 hydrogen bonds · protein-nucleic
D–B · 744 Å² buried · 18 hydrogen bonds · protein-nucleic
C–B · 496 Å² buried · 6 hydrogen bonds · protein-nucleic
C–D · 478 Å² buried · 38 hydrogen bonds · nucleic-nucleic

Compared structures

1EOP · Ecorv bound to cognate DNA · the same entry in another collection · chain B against B, 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 0.99

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 P04390
Elsewhere: RCSB PDB 1EOP · PDBe 1EOP · UniProt P04390

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