MolNFT v1 · #126388 · protein

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

5M1K · Phage terminase large subunit: “Crystal structure of the large terminase nuclease from thermophilic phage G20C with bound magnesium”. X-ray diffraction, 2 ligands (MG, SO4), 2 pockets (best druggability 0.83). MolNFT v1 #126388 on…

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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