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Gcnf DNA binding domain - OCT4 DR0 complex

Analyse Gcnf DNA binding domain - OCT4 DR0 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KRB
Type: protein + DNA
Length: 188 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)- 3'); Nuclear receptor…
UniProt: Q64249
Ligands: ZN
Pockets: 4 · best druggability 0.49

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(APGPAPGPGPTPCPAPAPGPGPCPTPAPGPA)- 3')	dna	16	—	—
B	Nuclear receptor subfamily 6 group a member 1	protein	74	39% helix, 8% strand	Q64249
E	DNA (5'-D(TPCPTPAPGPCPCPTPTPGPAPCPCPTPCPT)- 3')	dna	16	—	—
G	Nuclear receptor subfamily 6 group a member 1	protein	82	35% helix, 7% strand	Q64249

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains B, G

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.49	0.80	20	empty
2	93	0.46	0.81	16	empty
3	142	0.44	0.77	23	empty
4	56	0.25	0.73	8	empty

Interfaces

6 interfaces between chains.

A–E · 705 Å² buried · 69 hydrogen bonds · nucleic-nucleic
E–G · 648 Å² buried · 21 hydrogen bonds · protein-nucleic
A–G · 534 Å² buried · 12 hydrogen bonds · protein-nucleic
B–E · 434 Å² buried · 19 hydrogen bonds · protein-nucleic
A–B · 278 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

5KRB · GCNF DNA Binding Domain - Oct4 DR0 Complex · the same entry in another collection · chain A against A, TM-score 1.00
Q64249 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 6 group a member 1… · a predicted model of the same protein · chain B 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 Q64249
Elsewhere: RCSB PDB 5KRB · PDBe 5KRB · UniProt Q64249

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