MolNFT v1 · #31166 · protein + DNA

Ternary complex of hpoli with DNA and dctp

2ALZ · 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3': “Ternary complex of hpoli with DNA and dctp”. X-ray diffraction, 2 ligands (DCP, MG), 6 pockets (best druggability 0.77). MolNFT v1 #31166 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2ALZ
Type: protein + DNA
Length: 389 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'; 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'; DNA polymerase…
EC: 2.7.7.7
UniProt: Q9UNA4
Ligands: DCP, MG
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	5'-D(TPGPGPGPGPTPCPCP*T)-3'	dna	9	—	—
P	5'-D(APGPGPAPCPCP*(DOC))-3'	dna	7	—	—
A	DNA polymerase iota (EC 2.7.7.7)	protein	373	45% helix, 19% strand	Q9UNA4

Ligands and binding sites

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

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1163	0.77	0.79	87	MG, DCP
2	713	0.73	0.79	53	empty
3	72	0.38	0.78	15	empty
4	67	0.38	0.78	13	empty
5	105	0.35	0.73	18	empty

Interfaces

3 interfaces between chains.

T–A · 779 Å² buried · 13 hydrogen bonds · protein-nucleic
P–A · 482 Å² buried · 11 hydrogen bonds · protein-nucleic
T–P · 322 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2ALZ · Ternary Complex of hPoli with DNA and dCTP · the same entry in another collection · chain T against T, TM-score 1.00
Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · 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 Q9UNA4
Elsewhere: RCSB PDB 2ALZ · PDBe 2ALZ · UniProt Q9UNA4

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