MolNFT v1 · #158132 · protein + DNA

Ternary complex crystal structure of DNA polymerase beta with "hot- spot sequence" with beta-gamma chf analogue of dgtp

6NKV: “Ternary complex crystal structure of DNA polymerase beta with "hot- spot sequence" with beta-gamma chf…”. X-ray diffraction, 4 ligands (GFH, NA, MG). MolNFT v1 #158132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NKV
Type: protein + DNA
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: P06746
Ligands: GFH, NA, MG, CL

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	—	dna	16	—	—
P	—	dna	10	—	—
D	—	dna	5	—	—
A	—	protein	326	—	P06746

Ligands and binding sites

GFH · 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono) methyl](hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]guanosine · ligand · chains T, P, A
NA · Sodium ion · metal · 3 copies · chains P, A, D
MG · Magnesium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 3 copies · chains A

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

Compared structures

6NKV · Ternary complex crystal structure of DNA polymerase Beta with hot-spot sequence" with… · the same entry in another collection · chain T against T, TM-score 1.00
P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P06746
Elsewhere: RCSB PDB 6NKV · PDBe 6NKV · UniProt P06746

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