MolNFT v1 · #175856 · protein + DNA

Crystal structure of OSPHR2 in complex with DNA

7D3T · Protein phosphate starvation response 2: “Crystal structure of OSPHR2 in complex with DNA”. X-ray diffraction, 6 pockets (best druggability 0.67). MolNFT v1 #175856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7D3T
Type: protein + DNA
Length: 303 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein phosphate starvation response 2; DNA (5'…
UniProt: B8B5N8
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 59% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein phosphate starvation response 2	protein	59	63% helix, 0% strand	B8B5N8
D	Protein phosphate starvation response 2	protein	62	55% helix, 0% strand	B8B5N8
E, G	DNA (5'- D(PGPCPTPTPGPAPGPGPAPTPAPTPCPCPGPA)-3')	dna	16	—	—
F, H	DNA (5'- D(PCPTPCPGPGPAPTPAPTPCPCPTPCPAPAPG)-3')	dna	16	—	—

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	277	0.67	0.83	38	empty
2	197	0.63	0.83	30	empty
3	88	0.58	0.87	19	empty
4	83	0.41	0.79	18	empty
5	68	0.31	0.75	13	empty

Interfaces

14 interfaces between chains.

E–F · 700 Å² buried · 59 hydrogen bonds · nucleic-nucleic
G–H · 693 Å² buried · 55 hydrogen bonds · nucleic-nucleic
A–F · 507 Å² buried · 7 hydrogen bonds · protein-nucleic
D–H · 500 Å² buried · 7 hydrogen bonds · protein-nucleic
C–H · 494 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

7D3T · Crystal structure of OSPHR2 in complex with DNA · the same entry in another collection · chain H against H, TM-score 1.00
B8B5N8 · AlphaFold monomer V2.0 prediction for protein phosphate starvation response 2 (B8B5N8) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 B8B5N8
Elsewhere: RCSB PDB 7D3T · PDBe 7D3T · UniProt B8B5N8

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