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Strong hydrogen bonds in photoactive yellow protein and their role in its photocycle

Analyse Strong hydrogen bonds in photoactive yellow protein and their role in its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OTD
Type: protein
Length: 210 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photoactive yellow protein
UniProt: P16113
Ligands: HC4
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Photoactive yellow protein	protein	105	30% helix, 33% strand	P16113

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.63	0.80	28	HC4

Interfaces

1 interface between chains.

A–B · 600 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1OTD · Strong hydrogen bonds in photoactive yellow protein and their role in its photocycle · 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 P16113
Elsewhere: RCSB PDB 1OTD · PDBe 1OTD · UniProt P16113

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