MolNFT v1 · #121334 · protein

Crystal structure of the quinone-bound yodb from B. subtilis

5HS9 · Hth-type transcriptional regulator yodb: “Crystal structure of the quinone-bound yodb from B. subtilis”. X-ray diffraction, 2 pockets (best druggability 0.45). MolNFT v1 #121334 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5HS9
Type: protein
Length: 178 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hth-type transcriptional regulator yodb
UniProt: O34844
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hth-type transcriptional regulator yodb	protein	88	65% helix, 10% strand	O34844
B	Hth-type transcriptional regulator yodb	protein	90	61% helix, 11% strand	O34844

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.45	0.80	15	empty
2	50	0.35	0.79	13	empty

Interfaces

1 interface between chains.

A–B · 1442 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5HS9 · Crystal structure of the qui -bound YodB from B. subtilis · the same entry in another collection · chain A against A, TM-score 1.00
O34844 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator yodb (O34844) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O34844
Elsewhere: RCSB PDB 5HS9 · PDBe 5HS9 · UniProt O34844

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