MolNFT v1 · #116056 · protein + DNA

The crystal structure of stpr from bombyx mori in complex with 13-bp DNA derived from the +290 site of fibroin gene

5D23 · Fibroin-modulator-binding protein-1: “The crystal structure of stpr from bombyx mori in complex with 13-bp DNA derived from the +290 site of…”. X-ray diffraction, 2 pockets (best druggability 0.64). MolNFT v1 #116056 on GenesisL1…

PDB: 5D23
Type: protein + DNA
Length: 90 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibroin-modulator-binding protein-1; DNA (26-mer)
UniProt: Q5FBS0
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 91% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibroin-modulator-binding protein-1	protein	64	91% helix, 0% strand	Q5FBS0
B	DNA (26-mer)	dna	26	—	—

Pockets

2 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	220	0.64	0.83	30	empty
2	242	0.62	0.81	24	empty

Interfaces

1 interface between chains.

A–B · 1221 Å² buried · 22 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

5D23 · The crystal structure of STPR from Bombyx mori in complex with 13-bp DNA derived from the… · 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 5D23 · PDBe 5D23 · UniProt Q5FBS0

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