MolNFT v1 · #26572 · protein

Crystal structure of type II restrcition endonuclease, ECOO109I DNA- free form

1WTD · ECOO109IR: “Crystal structure of type II restrcition endonuclease, ECOO109I DNA- free form”. X-ray diffraction, 7 pockets (best druggability 0.67). MolNFT v1 #26572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1WTD
Type: protein
Length: 531 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ECOO109IR
EC: 3.1.21.4
UniProt: Q9RPJ3
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ECOO109IR (EC 3.1.21.4)	protein	264	54% helix, 10% strand	Q9RPJ3
B	ECOO109IR (EC 3.1.21.4)	protein	267	58% helix, 7% strand	Q9RPJ3

Ligands and binding sites

GOL · Glycerol · additive · 10 copies · chains A, B

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

Pockets

7 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	451	0.67	0.79	36	GOL
2	51	0.49	0.87	18	empty
3	144	0.47	0.77	29	GOL
4	124	0.44	0.77	25	GOL
5	88	0.42	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 2814 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

1WTD · Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form · 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 Q9RPJ3
Elsewhere: RCSB PDB 1WTD · PDBe 1WTD · UniProt Q9RPJ3

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