MolNFT v1 · #124904 · protein + DNA

Teranry complex of human DNA polymerase iota R96G inserting dcmpnpp opposite template G in the presence of MN2+

5KT5 · DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'): “Teranry complex of human DNA polymerase iota R96G inserting dcmpnpp opposite template G in the presence of…”. X-ray diffraction, 2 ligands (0KX, MN), 3 pockets (best druggability 0.74).…

PDB: 5KT5
Type: protein + DNA
Length: 396 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'); DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'); DNA…
EC: 2.7.7.7
UniProt: Q9UNA4
Ligands: 0KX, MN
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(CPTPGPGPGPGPTPCPCPT)-3')	dna	10	—	—
P	DNA (5'-D(PAPGPGPAPCPCP*C)-3')	dna	7	—	—
A	DNA polymerase iota (EC 2.7.7.7)	protein	379	47% helix, 20% strand	Q9UNA4

Ligands and binding sites

0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains T, P, A
MN · Manganese (II) ion · metal · 2 copies · chains P, A

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

Pockets

3 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	712	0.74	0.80	58	empty
2	479	0.66	0.78	44	0KX
3	469	0.65	0.78	36	empty

Interfaces

3 interfaces between chains.

T–A · 920 Å² buried · 16 hydrogen bonds · protein-nucleic
P–A · 518 Å² buried · 12 hydrogen bonds · protein-nucleic
T–P · 329 Å² buried · 22 hydrogen bonds · nucleic-nucleic

Compared structures

5KT5 · Teranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G… · 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 1.00

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 5KT5 · PDBe 5KT5 · UniProt Q9UNA4

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