MolNFT v1 · #109359 · protein + DNA

Structure of BSG25A binding with DNA

4X0G · Blastoderm-specific gene 25A: “Structure of BSG25A binding with DNA”. X-ray diffraction, 11 pockets (best druggability 0.86). MolNFT v1 #109359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X0G
Type: protein + DNA
Length: 486 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blastoderm-specific gene 25A; DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
UniProt: Q9VR17
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Blastoderm-specific gene 25A	protein	108	54% helix, 9% strand	Q9VR17
B, C	Blastoderm-specific gene 25A	protein	109	52% helix, 9% strand	Q9VR17
E, F, G, H	DNA (5'-D(GPTPTPCPCPAPAPTPTPGPGPAP*A)-3')	dna	13	—	—

Ligands and binding sites

ACT · Acetate ion · additive · 3 copies · chains A, D

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.86	0.87	70	empty
2	565	0.83	0.89	47	empty
3	101	0.43	0.79	19	empty
4	120	0.42	0.77	16	empty
5	50	0.41	0.83	12	empty

Interfaces

21 interfaces between chains.

B–F · 665 Å² buried · 18 hydrogen bonds · protein-nucleic
C–G · 655 Å² buried · 17 hydrogen bonds · protein-nucleic
D–H · 623 Å² buried · 16 hydrogen bonds · protein-nucleic
A–E · 606 Å² buried · 12 hydrogen bonds · protein-nucleic
G–H · 547 Å² buried · 54 hydrogen bonds · nucleic-nucleic

Compared structures

4X0G · Structure of Bsg25A binding with DNA · the same entry in another collection · chain H against H, TM-score 1.00
Q9VR17 · AlphaFold monomer V2.0 prediction for early boundary activity protein 1 (Q9VR17) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 Q9VR17
Elsewhere: RCSB PDB 4X0G · PDBe 4X0G · UniProt Q9VR17

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