MolNFT v1 · #74698 · protein

Structures of archaeal members of the ligd 3'-phosphoesterase DNA repair enzyme superfamily

3P4H · ATP-dependent DNA ligase, N-terminal domain protein: “Structures of archaeal members of the ligd 3'-phosphoesterase DNA repair enzyme superfamily”. X-ray diffraction, 2 ligands (MN, PO4), 1 pocket (best druggability 0.40). MolNFT v1…

PDB: 3P4H
Type: protein
Length: 118 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent DNA ligase, N-terminal domain protein
UniProt: B1L4V6
Ligands: MN, PO4
Pockets: 1 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 64% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent DNA ligase, N-terminal domain protein	protein	118	4% helix, 64% strand	B1L4V6

Ligands and binding sites

MN · Manganese (II) ion · metal · chains A
PO4 · Phosphate ion · ion · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.40	0.75	21	MN, PO4

Compared structures

3P4H · Structures of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme… · 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 B1L4V6
Elsewhere: RCSB PDB 3P4H · PDBe 3P4H · UniProt B1L4V6

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