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Structure of Prim-PolC from Mycobacterium smegmatis

Analyse Structure of Prim-PolC from Mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OP0
Type: protein
Length: 661 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.84
Source: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Molecule: DNA polymerase LigD, polymerase domain
UniProt: A0R5T1
Pockets: 8 · best druggability 0.50

Structure

x-ray diffraction · resolution 1.84 · 2 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA polymerase LigD, polymerase domain	protein	331	31% helix, 21% strand	A0R5T1
A	DNA polymerase LigD, polymerase domain	protein	330	31% helix, 22% strand	A0R5T1

Pockets

8 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	57	0.50	0.86	16	empty
2	57	0.48	0.85	17	empty
3	176	0.44	0.74	33	empty
4	142	0.44	0.76	22	empty
5	128	0.40	0.75	19	empty

Interfaces

1 interface between chains.

B–A · 426 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5OP0 · Structure of prim-polc from mycobacterium smegmatis · 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 A0R5T1
Elsewhere: RCSB PDB 5OP0 · PDBe 5OP0 · UniProt A0R5T1

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