MolNFT v1 · #68743 · protein + DNA

Crystal structure of E.COLI pol II-normal DNA-datp ternary complex

3K57 · DNA polymerase II: “Crystal structure of E.COLI pol II-normal DNA-datp ternary complex”. X-ray diffraction, 2 ligands (DTP, MG), 9 pockets (best druggability 0.78). MolNFT v1 #68743 on GenesisL1: 3D structure, binding sites and…

PDB: 3K57
Type: protein + DNA
Length: 812 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase II; DNA (5'- D(*G*TP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*G)-3')…
EC: 2.7.7.7
UniProt: P21189
Ligands: DTP, MG
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase II (EC 2.7.7.7)	protein	782	41% helix, 24% strand	P21189
T	DNA (5'- D(GTPAPTPGPTPAPCPGPCPTPAPGPGPCPAPCPG)-3')	dna	17	—	—
P	DNA (5'-D(GPTPGPCPCPTPAPGPCPGPTPAP*(DOC))-3')	dna	13	—	—

Ligands and binding sites

DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
MG · Magnesium ion · metal · 2 copies · chains A, P

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	140	0.78	0.96	32	empty
2	773	0.74	0.79	61	empty
3	718	0.72	0.79	75	DTP, MG
4	386	0.59	0.75	36	empty
5	104	0.52	0.82	23	empty

Interfaces

3 interfaces between chains.

A–T · 1398 Å² buried · 18 hydrogen bonds · protein-nucleic
A–P · 781 Å² buried · 17 hydrogen bonds · protein-nucleic
T–P · 626 Å² buried · 55 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3K57 · Crystal structure of E.coli Pol II-normal DNA-dATP ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
P21189 · AlphaFold monomer V2.0 prediction for DNA polymerase II (P21189) · a predicted model of the same protein · 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 P21189
Elsewhere: RCSB PDB 3K57 · PDBe 3K57 · UniProt P21189

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