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Structure of the dnag primase catalytic domain bound to ssdna

Analyse Structure of the dnag primase catalytic domain bound to ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B39
Type: protein + DNA
Length: 638 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3'); DNA primase
EC: 2.7.7.-
UniProt: P0ABS5
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'- D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3')	dna	5	—	—
D	DNA (5'- D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3')	dna	6	—	—
A	DNA primase (EC 2.7.7.-)	protein	317	50% helix, 17% strand	P0ABS5
B	DNA primase (EC 2.7.7.-)	protein	310	51% helix, 17% strand	P0ABS5

Pockets

8 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	1131	0.77	0.80	106	empty
2	299	0.55	0.76	43	empty
3	96	0.45	0.80	24	empty
4	99	0.45	0.79	20	empty
5	131	0.44	0.77	27	empty

Interfaces

5 interfaces between chains.

A–B · 627 Å² buried · 5 hydrogen bonds · protein-protein
C–A · 392 Å² buried · 5 hydrogen bonds · protein-nucleic
D–B · 390 Å² buried · 3 hydrogen bonds · protein-nucleic
C–B · 98 Å² buried · 0 hydrogen bonds · protein-nucleic
D–A · 92 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

3B39 · Structure of the DnaG primase catalytic domain bound to ssDNA · the same entry in another collection · chain C against C, TM-score 1.00
P0ABS5 · AlphaFold monomer V2.0 prediction for DNA primase (P0ABS5) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0ABS5
Elsewhere: RCSB PDB 3B39 · PDBe 3B39 · UniProt P0ABS5

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