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Crystal structure of a DNA primase domain from pseudomonas aeruginosa

Analyse Crystal structure of a DNA primase domain from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VAZ
Type: protein
Length: 641 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase
EC: 2.7.7.-
UniProt: Q9I5W0
Ligands: SO4
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase (EC 2.7.7.-)	protein	320	49% helix, 18% strand	Q9I5W0
B	DNA primase (EC 2.7.7.-)	protein	321	49% helix, 17% strand	Q9I5W0

Ligands and binding sites

SO4 · Sulfate ion · ion · 15 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.78	0.91	34	SO4
2	574	0.64	0.76	47	SO4
3	173	0.62	0.84	29	empty
4	134	0.44	0.76	28	SO4
5	68	0.41	0.81	16	empty

Interfaces

1 interface between chains.

A–B · 772 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5VAZ · Crystal structure of a DNA primase domain from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
Q9I5W0 · AlphaFold monomer V2.0 prediction for DNA primase (Q9I5W0) · a predicted model of the same protein · chain B 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 Q9I5W0
Elsewhere: RCSB PDB 5VAZ · PDBe 5VAZ · UniProt Q9I5W0

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