MolNFT v1 · #15277 · protein

Crystal structure of the photoactive yellow protein domain from the sensor histidine kinase ppr from rhodospirillum centenum

1MZU: “Crystal structure of the photoactive yellow protein domain from the sensor histidine kinase ppr from…”. X-ray diffraction, 1 ligand (HC4), 4 pockets (best druggability 0.69). MolNFT v1 #15277 on GenesisL1: 3D structure, binding…

PDB: 1MZU
Type: protein
Length: 329 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ppr
UniProt: Q9X2W8
Ligands: HC4
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ppr	protein	107	32% helix, 36% strand	Q9X2W8
B	Ppr	protein	114	32% helix, 32% strand	Q9X2W8
C	Ppr	protein	108	35% helix, 28% strand	Q9X2W8

Ligands and binding sites

HC4 · 4'-hydroxycinnamic acid · ligand · 3 copies · chains A, B, C

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.69	0.87	31	empty
2	221	0.60	0.80	22	HC4
3	52	0.56	0.90	14	HC4
4	53	0.55	0.89	14	HC4

Interfaces

2 interfaces between chains.

B–C · 469 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 188 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

1MZU · Crystal Structure of the Photoactive Yellow Protein Domain from the Sensor Histidine… · 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 Q9X2W8
Elsewhere: RCSB PDB 1MZU · PDBe 1MZU · UniProt Q9X2W8

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