MolNFT v1 · #126393 · protein

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

5M1P · Terminase large subunit: “Crystal structure of the large terminase nuclease from thermophilic phage G20C with bound calcium”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.79). MolNFT v1 #126393 on GenesisL1: 3D…

PDB: 5M1P
Type: protein
Length: 376 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Terminase large subunit
Ligands: CA
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Terminase large subunit	protein	187	32% helix, 28% strand	—
B	Terminase large subunit	protein	189	31% helix, 27% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, 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	518	0.79	0.86	72	empty
2	109	0.38	0.75	20	CA

Interfaces

1 interface between chains.

A–B · 794 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5M1P · 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 5M1P · PDBe 5M1P

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