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Structure of the synthase subunit of plp synthase

Analyse Structure of the synthase subunit of plp synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZNN
Type: protein
Length: 1,470 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plp synthase
Ligands: SO4
Pockets: 13 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Plp synthase	protein	245	47% helix, 16% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.63	0.80	43	SO4, MRD
2	248	0.61	0.80	38	SO4, MRD
3	219	0.60	0.81	35	SO4, MRD
4	206	0.60	0.81	38	SO4, MRD
5	208	0.59	0.80	38	SO4, MRD

Interfaces

6 interfaces between chains.

E–F · 1003 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 999 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 994 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 974 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 973 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1ZNN · Structure of the synthase subunit of PLP synthase · 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
Elsewhere: RCSB PDB 1ZNN · PDBe 1ZNN

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