Research workbench

Ecorv-T93A/DNA/CA2+

Analyse Ecorv-T93A/DNA/CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BSS
Type: protein + DNA
Length: 480 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'; Ecorv endonuclease
EC: 3.1.21.4
UniProt: P04390
Ligands: CA
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-D(APAPAPGPAPTPAPTPCPTP*T)-3'	dna	11	—	—
A	Ecorv endonuclease (EC 3.1.21.4)	protein	230	33% helix, 31% strand	P04390
B	Ecorv endonuclease (EC 3.1.21.4)	protein	228	31% helix, 29% 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

5 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	945	0.85	0.87	87	CA
2	183	0.63	0.84	29	empty
3	209	0.53	0.78	27	empty
4	183	0.49	0.77	27	empty
5	68	0.33	0.76	10	empty

Interfaces

6 interfaces between chains.

A–B · 1384 Å² buried · 8 hydrogen bonds · protein-protein
D–B · 736 Å² buried · 11 hydrogen bonds · protein-nucleic
C–A · 724 Å² buried · 16 hydrogen bonds · protein-nucleic
C–D · 498 Å² buried · 43 hydrogen bonds · nucleic-nucleic
D–A · 471 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

1BSS · Ecorv-T93A/DNA/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 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 1BSS · PDBe 1BSS · UniProt P04390

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