MolNFT v1 · #30274 · protein + DNA

T7 DNA polymerase in complex with 8OG and incoming ddatp

1ZYQ · 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP…: “T7 DNA polymerase in complex with 8OG and incoming ddatp”. X-ray diffraction, 2 ligands (DAD, MG), 7 pockets (best druggability 0.79). MolNFT v1 #30274 on GenesisL1: 3D…

PDB: 1ZYQ
Type: protein + DNA
Length: 813 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP *CP*CP*AP*(DDG))-3'…
EC: 2.7.7.7
UniProt: P00581, P0AA25
Ligands: DAD, MG
Pockets: 7 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	5'-D(CPGPAPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGP CPCPAP(DDG))-3'	dna	13	—	—
T	5'-D(CPCPCP(8OG) PCPTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPTPCPG)- 3'	dna	15	—	—
A	DNA polymerase (EC 2.7.7.7)	protein	680	47% helix, 14% strand	P00581
B	Thioredoxin 1	protein	105	33% helix, 29% strand	P0AA25

Ligands and binding sites

DAD · 2',3'-dideoxyadenosine-5'-triphosphate · ligand · chains P, T, A
MG · Magnesium ion · metal · 3 copies · chains A, P

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

Pockets

7 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	1127	0.79	0.81	100	MG, DAD
2	711	0.74	0.80	65	MG
3	626	0.70	0.79	57	empty
4	138	0.47	0.77	23	empty
5	127	0.46	0.78	18	empty

Interfaces

4 interfaces between chains.

T–A · 1135 Å² buried · 27 hydrogen bonds · protein-nucleic
A–B · 1057 Å² buried · 11 hydrogen bonds · protein-protein
P–A · 797 Å² buried · 14 hydrogen bonds · protein-nucleic
P–T · 608 Å² buried · 50 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

1ZYQ · T7 DNA polymerase in complex with 8oG and incoming ddATP · the same entry in another collection · chain A against A, 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 1ZYQ · PDBe 1ZYQ · UniProt P00581 · UniProt P0AA25

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