MolNFT v1 · #68744 · protein + DNA

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

3K58 · DNA polymerase II: “Crystal structure of E.COLI pol II-normal DNA-dttp ternary complex”. X-ray diffraction, 2 ligands (TTP, MG), 9 pockets (best druggability 0.78). MolNFT v1 #68744 on GenesisL1: 3D structure, binding sites and…

PDB: 3K58
Type: protein + DNA
Length: 810 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase II; DNA (5'- D(*TP*AP*AP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')…
EC: 2.7.7.7
UniProt: P21189
Ligands: TTP, MG
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase II (EC 2.7.7.7)	protein	780	41% helix, 25% strand	P21189
T	DNA (5'- D(TPAPAPGPTPAPCPGPCPTPAPGPGPCPAPCP*A)-3')	dna	17	—	—
P	DNA (5'-D(GPTPGPCPCPTPAPGPCPGPTPAP*(DOC))-3')	dna	13	—	—

Ligands and binding sites

TTP · Thymidine-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	131	0.78	0.97	28	empty
2	1114	0.76	0.79	82	empty
3	302	0.63	0.80	38	TTP, MG
4	308	0.55	0.75	39	empty
5	237	0.53	0.76	37	empty

Interfaces

3 interfaces between chains.

A–T · 1412 Å² buried · 17 hydrogen bonds · protein-nucleic
A–P · 782 Å² buried · 20 hydrogen bonds · protein-nucleic
T–P · 613 Å² buried · 54 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3K58 · Crystal structure of E.coli Pol II-normal DNA-dTTP 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 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 P21189
Elsewhere: RCSB PDB 3K58 · PDBe 3K58 · UniProt P21189

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