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Human DNA polymerase beta complexed with gapped DNA and ddctp

Analyse Human DNA polymerase beta complexed with gapped DNA and ddctp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BPY
Type: protein + DNA
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC: 2.7.7.7
UniProt: P06746
Ligands: DCT, MG, NA
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPDOC)-3')	dna	10	—	—
D	DNA (5'-D(GPTPCPGP*G)-3')	dna	5	—	—
A	Protein (DNA polymerase beta) (EC 2.7.7.7)	protein	326	50% helix, 12% strand	P06746

Ligands and binding sites

DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains T, P, A
MG · Magnesium ion · metal · 2 copies · chains A, P
NA · Sodium ion · metal · 2 copies · chains P, A, D

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	1033	0.72	0.76	64	MG, NA, DCT
2	407	0.63	0.78	28	empty
3	172	0.57	0.81	22	empty

Interfaces

5 interfaces between chains.

T–A · 716 Å² buried · 13 hydrogen bonds · protein-nucleic
T–P · 476 Å² buried · 55 hydrogen bonds · nucleic-nucleic
D–A · 391 Å² buried · 12 hydrogen bonds · protein-nucleic
P–A · 359 Å² buried · 11 hydrogen bonds · protein-nucleic
T–D · 226 Å² buried · 18 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

1BPY · Human DNA polymerase beta complexed with gapped DNA and ddctp · 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 0.95

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 1BPY · PDBe 1BPY · UniProt P06746

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