MolNFT v1 · #181618 · protein + DNA

Pre-catalytic ternary complex of DNA polymerase lambda with bound 1-nt gapped ssb substrate and incoming dumpnpp

7M07: “Pre-catalytic ternary complex of DNA polymerase lambda with bound 1-nt gapped ssb substrate and incoming…”. X-ray diffraction, 4 ligands (DUP, NA, MG). MolNFT v1 #181618 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7M07
Type: protein + DNA
Length: 348 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q9UGP5
Ligands: DUP, NA, MG, CL

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	327	—	Q9UGP5
T	—	dna	11	—	—
P	—	dna	6	—	—
D	—	dna	4	—	—

Ligands and binding sites

DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
NA · Sodium ion · metal · 5 copies · chains A, P, D, T
MG · Magnesium ion · metal · 2 copies · chains A, P
CL · Chloride ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Compared structures

7M07 · Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB… · the same entry in another collection · chain A against A, TM-score 1.00
Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9UGP5
Elsewhere: RCSB PDB 7M07 · PDBe 7M07 · UniProt Q9UGP5

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