MolNFT v1 · #17933 · protein

New crystal structure of chlorella virus DNA ligase-adenylate

1P8L · Pbcv-1 DNA ligase: “New crystal structure of chlorella virus DNA ligase-adenylate”. X-ray diffraction, 1 ligand (AMP), 2 pockets (best druggability 0.55). MolNFT v1 #17933 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1P8L
Type: protein
Length: 276 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pbcv-1 DNA ligase
UniProt: O41026
Ligands: AMP
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pbcv-1 DNA ligase	protein	276	18% helix, 29% strand	O41026

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A

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	152	0.55	0.81	30	AMP
2	63	0.30	0.74	15	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1P8L · New Crystal Structure of Chlorella Virus DNA Ligase-Adenylate · 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 O41026
Elsewhere: RCSB PDB 1P8L · PDBe 1P8L · UniProt O41026

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