MolNFT v1 · #22545 · protein + DNA

T7 DNA polymerase ternary complex with dctp at the insertion site.

1T8E · 5'- D(P*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*G…: “T7 DNA polymerase ternary complex with dctp at the insertion site.”. X-ray diffraction, 3 ligands (DCT, MG, SO4), 10 pockets (best druggability 0.73). MolNFT v1 #22545…

PDB: 1T8E
Type: protein + DNA
Length: 851 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- D(P*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*C P*CP*AP*(2DT))-3'…
EC: 2.7.7.7
UniProt: P00581, P0AA25
Ligands: DCT, MG, SO4
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'- D(PCPGPAPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPC PCPAP(2DT))-3'	dna	22	—	—
D	25-mer	dna	25	—	—
A	DNA polymerase (EC 2.7.7.7)	protein	698	46% helix, 14% strand	P00581
B	Thioredoxin 1	protein	106	36% helix, 27% strand	P0AA25

Ligands and binding sites

DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains C, D, A
MG · Magnesium ion · metal · 3 copies · chains A, C
SO4 · Sulfate ion · ion · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	709	0.73	0.79	70	MG, SO4, PG4
2	764	0.72	0.78	60	MG, DCT
3	598	0.71	0.79	49	empty
4	312	0.69	0.84	30	empty
5	241	0.56	0.79	22	empty

Interfaces

5 interfaces between chains.

D–A · 1485 Å² buried · 27 hydrogen bonds · protein-nucleic
A–B · 1085 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 970 Å² buried · 78 hydrogen bonds · nucleic-nucleic
C–A · 968 Å² buried · 19 hydrogen bonds · protein-nucleic
C–B · 69 Å² buried · 3 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

1T8E · T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site. · the same entry in another collection · chain C against C, TM-score 1.00
P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P00581
Every structure of UniProt P0AA25
Elsewhere: RCSB PDB 1T8E · PDBe 1T8E · UniProt P00581 · UniProt P0AA25

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