MolNFT v1 · #180237 · protein + DNA

DNA polymerase mu, 8-OXODGTP:CT reaction state ternary complex, 10 mm MN2+ (40MIN)

7KTB: “DNA polymerase mu, 8-OXODGTP:CT reaction state ternary complex, 10 mm MN2+ (40MIN)”. X-ray diffraction, 4 ligands (8DG, PPV, MN). MolNFT v1 #180237 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KTB
Type: protein + DNA
Length: 343 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q9NP87
Ligands: 8DG, PPV, MN, NA

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	325	—	Q9NP87
T	—	dna	9	—	—
P	—	dna	5	—	—
D	—	dna	4	—	—

Ligands and binding sites

8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · chains A, T, P
PPV · Pyrophosphate · ligand · chains A, P
MN · Manganese (II) ion · metal · 9 copies · chains A, P, D, T
NA · Sodium ion · metal · chains A, P
EDO · 1,2-ethanediol · additive · 5 copies · chains A, P
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A

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

Compared structures

7KTB · DNA Polymerase Mu, 8-oxodGTP:Ct Reaction State Ternary Complex, 10 mM Mn2+ (40min) · the same entry in another collection · chain A against A, TM-score 1.00
Q9NP87 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9NP87) · 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 Q9NP87
Elsewhere: RCSB PDB 7KTB · PDBe 7KTB · UniProt Q9NP87

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