MolNFT v1 · #1915 · protein + DNA

Ecorv endonuclease complex with 5'-cgggatatccc DNA

1BGB · DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3'): “Ecorv endonuclease complex with 5'-cgggatatccc DNA”. X-ray diffraction, 3 pockets (best druggability 0.84). MolNFT v1 #1915 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1BGB
Type: protein + DNA
Length: 486 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3'); Ecorv endonuclease
EC: 3.1.21.4
UniProt: P04390
Pockets: 3 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'-D(CPGPGPGPAPTPAPTPCPCP*C)-3')	dna	11	—	—
D	DNA (5'-D(CPGPGPGPAPTPAPTPCPCP*C)-3')	dna	10	—	—
A	Ecorv endonuclease (EC 3.1.21.4)	protein	237	32% helix, 32% strand	P04390
B	Ecorv endonuclease (EC 3.1.21.4)	protein	228	30% helix, 31% strand	P04390

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	776	0.84	0.87	71	empty
2	567	0.68	0.78	80	empty
3	58	0.29	0.75	14	empty

Interfaces

6 interfaces between chains.

A–B · 1539 Å² buried · 20 hydrogen bonds · protein-protein
C–B · 695 Å² buried · 9 hydrogen bonds · protein-nucleic
D–A · 667 Å² buried · 10 hydrogen bonds · protein-nucleic
C–D · 454 Å² buried · 44 hydrogen bonds · nucleic-nucleic
C–A · 441 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

1BGB · Ecorv endonuclease complex with 5'-cgggatatccc DNA · 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 1BGB · PDBe 1BGB · UniProt P04390

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