MolNFT v1 · #14158 · protein

Crystal structure of bacteriophage T7 endonuclease I with a wild-type active site and bound manganese ions

1M0D · Endodeoxyribonuclease I: “Crystal structure of bacteriophage T7 endonuclease I with a wild-type active site and bound manganese ions”. X-ray diffraction, 2 ligands (MN, SO4), 5 pockets (best druggability 0.53). MolNFT v1 #14158 on…

PDB: 1M0D
Type: protein
Length: 516 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endodeoxyribonuclease I
EC: 3.1.21.2
UniProt: P00641
Ligands: MN, SO4
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Endodeoxyribonuclease I (EC 3.1.21.2)	protein	129	32% helix, 26% strand	P00641

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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	424	0.53	0.72	38	MN, SO4
2	114	0.41	0.76	24	empty
3	64	0.41	0.80	14	empty
4	57	0.40	0.81	21	empty
5	66	0.33	0.76	21	empty

Interfaces

5 interfaces between chains.

A–B · 3000 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 2833 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 337 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 326 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 125 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1M0D · Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and… · 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 P00641
Elsewhere: RCSB PDB 1M0D · PDBe 1M0D · UniProt P00641

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.