MolNFT v1 · #142946 · protein + DNA

Crystal structure of FOXC2 dbd bound to DBE2 DNA

6AKO · DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)…: “Crystal structure of FOXC2 dbd bound to DBE2 DNA”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.53). MolNFT v1 #142946 on GenesisL1: 3D structure…

PDB: 6AKO
Type: protein + DNA
Length: 129 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)- 3'); DNA…
UniProt: Q99958
Ligands: MG
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(CPAPAPAPAPTPGPTPAPAPAPCPAPAPGP*A)- 3')	dna	16	—	—
B	DNA (5'-D(TPCPTPTPGPTPTPTPAPCPAPTPTPTPTP*G)- 3')	dna	16	—	—
C	Forkhead box protein C2	protein	97	44% helix, 11% strand	Q99958

Ligands and binding sites

MG · Magnesium ion · metal · chains C

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

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	237	0.53	0.77	26	empty
2	112	0.34	0.73	13	empty
3	74	0.27	0.72	17	empty
4	51	0.27	0.75	14	empty

Interfaces

3 interfaces between chains.

A–B · 715 Å² buried · 56 hydrogen bonds · nucleic-nucleic
B–C · 557 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 452 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

6AKO · Crystal Structure of FOXC2 DBD Bound to DBE2 DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q99958 · AlphaFold monomer V2.0 prediction for forkhead box protein C2 (Q99958) · a predicted model of the same protein · chain C against A, TM-score 0.89

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 Q99958
Elsewhere: RCSB PDB 6AKO · PDBe 6AKO · UniProt Q99958

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