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DNA Polymerase Beta S229L crystallized in PEG 400

Analyse DNA Polymerase Beta S229L crystallized in PEG 400 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U8I
Type: protein + DNA
Length: 349 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.45
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: NA
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · resolution 2.45 · 4 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	318	51% helix, 13% strand	P06746
T	DNA (5'-D(CPCPGPAPCPAPGPCPGPCPAPTPCPAPGPC)-3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3')	dna	10	—	—
D	DNA (5'-D(GPTPCPGP*G)-3')	dna	5	—	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, D, P

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

Pockets

2 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	963	0.72	0.76	76	empty
2	181	0.59	0.83	25	empty

Interfaces

5 interfaces between chains.

T–P · 477 Å² buried · 49 hydrogen bonds · nucleic-nucleic
A–T · 445 Å² buried · 7 hydrogen bonds · protein-nucleic
A–P · 380 Å² buried · 8 hydrogen bonds · protein-nucleic
A–D · 330 Å² buried · 7 hydrogen bonds · protein-nucleic
T–D · 227 Å² buried · 21 hydrogen bonds · nucleic-nucleic

Compared structures

5U8I · DNA polymerase beta S229L crystallized in peg 400 · the same entry in another collection · chain A against A, TM-score 1.00
P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · 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 P06746
Elsewhere: RCSB PDB 5U8I · PDBe 5U8I · UniProt P06746

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