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Crystal structure of the RNA polymerase domain (rpd) of mycobacterium tuberculosis primase dnag

Analyse Crystal structure of the RNA polymerase domain (rpd) of mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W33
Type: protein
Length: 309 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase
EC: 2.7.7.-
UniProt: P9WNW1
Ligands: SO4
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase (EC 2.7.7.-)	protein	309	46% helix, 17% strand	P9WNW1

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

4 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	172	0.59	0.82	25	empty
2	70	0.36	0.77	15	empty
3	79	0.36	0.76	17	empty
4	72	0.31	0.74	20	SO4

Compared structures

5W33 · Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis… · the same entry in another collection · chain A against A, TM-score 1.00
P9WNW1 · AlphaFold monomer V2.0 prediction for DNA primase (P9WNW1) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P9WNW1
Elsewhere: RCSB PDB 5W33 · PDBe 5W33 · UniProt P9WNW1

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