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Crystal structure of the large terminase nuclease from thermophilic phage G20C with bound magnesium

Analyse Crystal structure of the large terminase nuclease from thermophilic phage G20C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M1K
Type: protein
Length: 378 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phage terminase large subunit
Ligands: MG, SO4
Pockets: 2 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phage terminase large subunit	protein	189	32% helix, 27% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · chains B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

2 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	697	0.83	0.87	77	empty
2	104	0.34	0.73	22	MG

Interfaces

1 interface between chains.

A–B · 785 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5M1K · Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound… · 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
Elsewhere: RCSB PDB 5M1K · PDBe 5M1K

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