MolNFT v1 · #48507 · protein + DNA

Pvuii endonuclease complexed to an iodinated cognate DNA

2PVI · DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3'): “Pvuii endonuclease complexed to an iodinated cognate DNA”. X-ray diffraction, 8 pockets (best druggability 0.67). MolNFT v1 #48507 on GenesisL1: 3D structure, binding sites…

PDB: 2PVI
Type: protein + DNA
Length: 338 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3'); Type II restriction enzyme…
EC: 3.1.21.4
UniProt: P23657
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'-D(TPGPAPCPCPAPGP(C38)PTPGPGPTP*C)-3')	dna	13	—	—
A, B	Type II restriction enzyme pvuii (EC 3.1.21.4)	protein	156	40% helix, 22% strand	P23657

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.67	0.83	22	empty
2	247	0.67	0.84	21	empty
3	122	0.60	0.86	22	empty
4	89	0.60	0.88	19	empty
5	70	0.58	0.89	18	empty

Interfaces

6 interfaces between chains.

A–B · 1726 Å² buried · 13 hydrogen bonds · protein-protein
C–B · 729 Å² buried · 15 hydrogen bonds · protein-nucleic
D–A · 723 Å² buried · 16 hydrogen bonds · protein-nucleic
C–D · 613 Å² buried · 45 hydrogen bonds · nucleic-nucleic
D–B · 474 Å² buried · 10 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2PVI · Pvuii endonuclease complexed to an iodinated cognate DNA · the same entry in another collection · chain C against C, TM-score 1.00
P23657 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme pvuii (P23657) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P23657
Elsewhere: RCSB PDB 2PVI · PDBe 2PVI · UniProt P23657

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