MolNFT v1 · #52586 · protein

Crystal structure of the dnai

2W58 · Primosome component (helicase loader): “Crystal structure of the dnai”. X-ray diffraction, 3 ligands (ADP, MG, PO4), 3 pockets (best druggability 0.69). MolNFT v1 #52586 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2W58
Type: protein
Length: 376 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Primosome component (helicase loader)
UniProt: Q5KWD0
Ligands: ADP, MG, PO4
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Primosome component (helicase loader)	protein	188	47% helix, 16% strand	Q5KWD0
B	Primosome component (helicase loader)	protein	188	47% helix, 15% strand	Q5KWD0

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
PO4 · Phosphate ion · ion · chains B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	344	0.69	0.82	41	ADP, MG
2	53	0.56	0.89	15	empty
3	103	0.47	0.80	21	empty

Interfaces

1 interface between chains.

A–B · 811 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2W58 · Crystal Structure of the DnaI · the same entry in another collection · chain B against B, 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 Q5KWD0
Elsewhere: RCSB PDB 2W58 · PDBe 2W58 · UniProt Q5KWD0

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