MolNFT v1 · #116078 · protein + DNA

Crystal structure of stpr from bombyx mori in complex with 20-bp DNA derived from +290 site of the fibroin gene

5D2Q · Fibroin-modulator-binding protein-1: “Crystal structure of stpr from bombyx mori in complex with 20-bp DNA derived from +290 site of the fibroin…”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #116078 on…

PDB: 5D2Q
Type: protein + DNA
Length: 117 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibroin-modulator-binding protein-1; DNA (40-mer)
UniProt: Q5FBS0
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibroin-modulator-binding protein-1	protein	77	77% helix, 0% strand	Q5FBS0
B	DNA (40-mer)	dna	40	—	—

Pockets

4 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	288	0.55	0.76	23	empty
2	230	0.54	0.77	21	empty
3	143	0.48	0.78	18	empty
4	64	0.26	0.72	15	empty

Interfaces

1 interface between chains.

A–B · 1427 Å² buried · 12 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

5D2Q · Crystal structure of STPR from Bombyx Mori in complex with 20-bp DNA derived from +290… · 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 5D2Q · PDBe 5D2Q · UniProt Q5FBS0

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