MolNFT v1 · #20950 · protein + DNA

Complex of ecorv endonuclease with D(AAAGAT)/D(ATCTT)

1RV5 · 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3': “Complex of ecorv endonuclease with D(AAAGAT)/D(ATCTT)”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #20950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1RV5
Type: protein + DNA
Length: 489 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'; Ecorv endonuclease
EC: 3.1.21.4
UniProt: P04390
Pockets: 5 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-D(APAPAPGPAPTAPTPCPTP*T)-3'	dna	11	—	—
A	Ecorv endonuclease (EC 3.1.21.4)	protein	240	31% helix, 31% strand	P04390
B	Ecorv endonuclease (EC 3.1.21.4)	protein	227	31% helix, 31% strand	P04390

Pockets

5 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	604	0.82	0.87	69	empty
2	161	0.59	0.83	28	empty
3	287	0.57	0.78	38	empty
4	161	0.55	0.81	24	empty
5	65	0.33	0.77	12	empty

Interfaces

6 interfaces between chains.

A–B · 1813 Å² buried · 26 hydrogen bonds · protein-protein
C–A · 696 Å² buried · 13 hydrogen bonds · protein-nucleic
D–B · 692 Å² buried · 13 hydrogen bonds · protein-nucleic
C–B · 500 Å² buried · 13 hydrogen bonds · protein-nucleic
C–D · 495 Å² buried · 40 hydrogen bonds · nucleic-nucleic

Compared structures

1RV5 · Complex of ecorv endonuclease with D(AAAGAT)/D(ATCTT) · 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 1RV5 · PDBe 1RV5 · UniProt P04390

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