MolNFT v1 · #1681 · protein + DNA

Restriction endonuclease ecorv with calcium

1B94 · DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'): “Restriction endonuclease ecorv with calcium”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.85). MolNFT v1 #1681 on GenesisL1: 3D structure, binding sites and…

PDB: 1B94
Type: protein + DNA
Length: 510 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'); Restriction endonuclease ecorv
EC: 3.1.21.4
UniProt: P04390
Ligands: CA
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'-D(APAPAPGPAPTPAPTPCPTP*T)-3')	dna	11	—	—
A, B	Restriction endonuclease ecorv (EC 3.1.21.4)	protein	244	34% helix, 29% 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	590	0.85	0.91	70	empty
2	171	0.57	0.81	26	empty
3	260	0.56	0.78	38	empty
4	165	0.53	0.80	28	empty
5	60	0.30	0.76	11	empty

Interfaces

6 interfaces between chains.

A–B · 2116 Å² buried · 30 hydrogen bonds · protein-protein
C–A · 769 Å² buried · 15 hydrogen bonds · protein-nucleic
D–B · 743 Å² buried · 14 hydrogen bonds · protein-nucleic
C–B · 542 Å² buried · 15 hydrogen bonds · protein-nucleic
D–A · 521 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

1B94 · Restriction endonuclease ecorv with calcium · 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 1B94 · PDBe 1B94 · UniProt P04390

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