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DNA polymerase beta matched substrate complex with CA2+, 0 S

Analyse DNA polymerase beta matched substrate complex with CA2+, 0 S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KLD
Type: protein + DNA
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: DCP, CA, NA, CL
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)-3'	dna	16	—	—
P	5'-D(GPCPTPGPAPTPGPCPGPC)-3'	dna	10	—	—
D	5'-D(PGPTPCPGP*G)-3'	dna	5	—	—
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	326	49% helix, 13% strand	P06746

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
CA · Calcium ion · metal · 2 copies · chains A, P
NA · Sodium ion · metal · 2 copies · chains P, A, D
CL · Chloride ion · ion · 4 copies · chains A

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

Pockets

3 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	987	0.71	0.76	57	DCP, CA
2	316	0.61	0.79	30	empty
3	230	0.56	0.79	26	empty

Interfaces

5 interfaces between chains.

T–A · 690 Å² buried · 10 hydrogen bonds · protein-nucleic
T–P · 470 Å² buried · 39 hydrogen bonds · nucleic-nucleic
D–A · 375 Å² buried · 8 hydrogen bonds · protein-nucleic
P–A · 362 Å² buried · 10 hydrogen bonds · protein-nucleic
T–D · 196 Å² buried · 18 hydrogen bonds · nucleic-nucleic

Compared structures

4KLD · DNA polymerase beta matched substrate complex with Ca2+, 0 s · the same entry in another collection · chain T against T, 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 0.91

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 4KLD · PDBe 4KLD · UniProt P06746

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