MolNFT v1 · #116080 · protein + DNA

Crystal structure of stpr from bombyx mori in complex with 18-bp DNA containing four repetitive units of atac

5D2S · Fibroin-modulator-binding protein-1: “Crystal structure of stpr from bombyx mori in complex with 18-bp DNA containing four repetitive units of atac”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #116080 on…

PDB: 5D2S
Type: protein + DNA
Length: 127 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibroin-modulator-binding protein-1; DNA (36-mer)
UniProt: Q5FBS0
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibroin-modulator-binding protein-1	protein	91	87% helix, 0% strand	Q5FBS0
B	DNA (36-mer)	dna	36	—	—

Pockets

5 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	262	0.65	0.82	26	empty
2	160	0.51	0.79	21	empty
3	147	0.47	0.77	22	empty
4	51	0.34	0.79	15	empty
5	73	0.28	0.72	17	empty

Interfaces

1 interface between chains.

A–B · 1743 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

5D2S · Crystal structure of STPR from Bombyx mori in complex with 18-bp DNA containing four… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5FBS0
Elsewhere: RCSB PDB 5D2S · PDBe 5D2S · UniProt Q5FBS0

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