MolNFT v1 · #58777 · protein + DNA

DNA polymerase I/DNA complex

3BDP · DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*GP*CP*2DT)-3'): “DNA polymerase I/DNA complex”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.70). MolNFT v1 #58777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BDP
Type: protein + DNA
Length: 600 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*GP*CP*2DT)-3'); DNA…
EC: 2.7.7.7
UniProt: P52026
Ligands: SO4
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	DNA (5'-D(GPCPAPTPGPAPTPGPCP2DT)-3')	dna	10	—	—
T	DNA (5'-D(APGPCPAPTPCPAPTPGPC)-3')	dna	10	—	—
A	Protein (DNA polymerase I) (EC 2.7.7.7)	protein	580	55% helix, 13% strand	P52026

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A

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

Pockets

8 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	277	0.70	0.85	32	empty
2	409	0.69	0.81	44	empty
3	681	0.67	0.76	58	SO4
4	112	0.45	0.78	21	empty
5	143	0.43	0.75	17	empty

Interfaces

3 interfaces between chains.

T–A · 796 Å² buried · 10 hydrogen bonds · protein-nucleic
P–A · 791 Å² buried · 16 hydrogen bonds · protein-nucleic
P–T · 452 Å² buried · 45 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3BDP · DNA polymerase I/DNA complex · the same entry in another collection · chain P against P, TM-score 1.00
P52026 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P52026) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P52026
Elsewhere: RCSB PDB 3BDP · PDBe 3BDP · UniProt P52026

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