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Crystal structure of bacillus subtilis padr in complex with P-coumaric acid

Analyse Crystal structure of bacillus subtilis padr in complex with P-coumaric acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y8T
Type: protein
Length: 497 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator
UniProt: E0TW95
Ligands: HC4
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator	protein	162	72% helix, 1% strand	E0TW95
B	Transcriptional regulator	protein	169	69% helix, 6% strand	E0TW95
C	Transcriptional regulator	protein	166	67% helix, 5% strand	E0TW95

Ligands and binding sites

HC4 · 4'-hydroxycinnamic acid · ligand · 2 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.79	0.87	69	HC4
2	222	0.49	0.75	23	empty
3	89	0.40	0.77	21	empty
4	64	0.35	0.77	19	empty
5	59	0.35	0.78	12	HC4

Interfaces

2 interfaces between chains.

B–C · 3543 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 479 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5Y8T · Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt E0TW95
Elsewhere: RCSB PDB 5Y8T · PDBe 5Y8T · UniProt E0TW95

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