MolNFT v1 · #1353 · protein

Ecorv endonuclease, unliganded, form B, T93A mutant

1AZ4: “Ecorv endonuclease, unliganded, form B, T93A mutant”. X-ray diffraction, 8 pockets (best druggability 0.52). MolNFT v1 #1353 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1AZ4
Type: protein
Length: 402 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ecorv endonuclease
EC: 3.1.21.4
UniProt: P04390
Pockets: 8 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ecorv endonuclease (EC 3.1.21.4)	protein	187	22% helix, 27% strand	P04390
B	Ecorv endonuclease (EC 3.1.21.4)	protein	215	28% helix, 28% strand	P04390

Pockets

8 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	50	0.52	0.88	17	empty
2	152	0.45	0.75	24	empty
3	107	0.39	0.75	18	empty
4	116	0.39	0.75	26	empty
5	59	0.38	0.79	21	empty

Interfaces

1 interface between chains.

A–B · 987 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1AZ4 · Ecorv endonuclease, unliganded, form B, T93A mutant · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.96

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 1AZ4 · PDBe 1AZ4 · UniProt P04390

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