MolNFT v1 · #106456 · protein

DNA recognition domain of the cytosine modification-dependent restriction endonuclease lpnpi

4RZL: “DNA recognition domain of the cytosine modification-dependent restriction endonuclease lpnpi”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #106456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RZL
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Restriction endonuclease lpnpi
UniProt: Q5ZW53
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Restriction endonuclease lpnpi	protein	227	20% helix, 29% strand	Q5ZW53

Ligands and binding sites

1PE · Pentaethylene glycol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	337	0.65	0.80	47	empty
2	103	0.36	0.74	22	empty
3	84	0.34	0.75	19	empty
4	54	0.30	0.75	17	empty
5	52	0.29	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 369 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4RZL · DNA recognition domain of the cytosine modification-dependent restriction endonuclease… · the same entry in another collection · 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 Q5ZW53
Elsewhere: RCSB PDB 4RZL · PDBe 4RZL · UniProt Q5ZW53

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