MolNFT v1 · #170522 · protein

Minimal construct of CDC7-DBF4 bound to XL413

6YA6: “Minimal construct of CDC7-DBF4 bound to XL413”. X-ray diffraction, 4 ligands (0SX, ZN, BO3). MolNFT v1 #170522 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YA6
Type: protein
Length: 446 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: O00311, Q9UBU7
Ligands: 0SX, ZN, BO3, CL

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	344	—	O00311
B	—	protein	102	—	Q9UBU7

Ligands and binding sites

0SX · 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A, B
BO3 · Boric acid · ion · chains A
CL · Chloride ion · ion · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A
IMD · Imidazole · additive · chains B

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

Compared structures

6YA6 · Minimal construct of Cdc7-Dbf4 bound to XL413 · the same entry in another collection · chain A against A, TM-score 1.00
O00311 · AlphaFold monomer V2.0 prediction for cell division cycle 7-related protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q9UBU7 · AlphaFold monomer V2.0 prediction for protein DBF4 homolog a (Q9UBU7) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 O00311
Every structure of UniProt Q9UBU7
Elsewhere: RCSB PDB 6YA6 · PDBe 6YA6 · UniProt O00311 · UniProt Q9UBU7

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