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Crystal structure of biphenyl synthase from malus domestica

Analyse Crystal structure of biphenyl synthase from malus domestica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W8Q
Type: protein
Length: 757 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BIS3 biphenyl synthase
EC: 2.3.1.177
UniProt: K9MST3
Ligands: BU4
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BIS3 biphenyl synthase (EC 2.3.1.177)	protein	379	41% helix, 24% strand	K9MST3
B	BIS3 biphenyl synthase (EC 2.3.1.177)	protein	378	41% helix, 24% strand	K9MST3

Ligands and binding sites

BU4 · (3R)-butane-1,3-diol · ligand · 2 copies · chains A, B

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

Pockets

6 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	318	0.78	0.88	43	empty
2	322	0.75	0.87	51	empty
3	128	0.45	0.78	26	empty
4	105	0.39	0.76	23	empty
5	53	0.28	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 2367 Å² buried · 53 hydrogen bonds · protein-protein

Compared structures

5W8Q · Crystal structure of biphenyl synthase from Malus domestica · 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 K9MST3
Elsewhere: RCSB PDB 5W8Q · PDBe 5W8Q · UniProt K9MST3

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