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Ternary complex of human DNA polymerase iota with DNA and dttp

Analyse Ternary complex of human DNA polymerase iota with DNA and dttp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FLL
Type: protein + DNA
Length: 389 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primer strand; DNA template strand; DNA polymerase iota
EC: 2.7.7.7
UniProt: Q9UNA4
Ligands: TTP, MG
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	DNA primer strand	dna	7	—	—
T	DNA template strand	dna	9	—	—
A	DNA polymerase iota (EC 2.7.7.7)	protein	373	44% helix, 19% strand	Q9UNA4

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · chains P, T, A
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

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	634	0.74	0.81	52	empty
2	741	0.73	0.79	59	empty
3	373	0.70	0.82	38	MG, TTP
4	91	0.44	0.79	16	empty
5	75	0.41	0.79	13	empty

Interfaces

3 interfaces between chains.

T–A · 743 Å² buried · 15 hydrogen bonds · protein-nucleic
P–A · 488 Å² buried · 8 hydrogen bonds · protein-nucleic
P–T · 327 Å² buried · 24 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2FLL · Ternary complex of human DNA polymerase iota with DNA and dTTP · the same entry in another collection · chain P against P, 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 2FLL · PDBe 2FLL · UniProt Q9UNA4

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