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Crystal structure of plp-soaked hmp synthase THI5 from S. cerevisiae

Analyse Crystal structure of plp-soaked hmp synthase THI5 from S. cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4H6D
Type: protein
Length: 2,602 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrimidine precursor biosynthesis enzyme THI5
UniProt: P43534
Ligands: PLP
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Pyrimidine precursor biosynthesis enzyme THI5	protein	330	48% helix, 17% strand	P43534
A	Pyrimidine precursor biosynthesis enzyme THI5	protein	314	47% helix, 17% strand	P43534
B	Pyrimidine precursor biosynthesis enzyme THI5	protein	329	47% helix, 17% strand	P43534
C	Pyrimidine precursor biosynthesis enzyme THI5	protein	335	48% helix, 16% strand	P43534
D	Pyrimidine precursor biosynthesis enzyme THI5	protein	333	47% helix, 17% strand	P43534
E	Pyrimidine precursor biosynthesis enzyme THI5	protein	302	46% helix, 18% strand	P43534
G	Pyrimidine precursor biosynthesis enzyme THI5	protein	331	47% helix, 17% strand	P43534
H	Pyrimidine precursor biosynthesis enzyme THI5	protein	328	48% helix, 17% strand	P43534

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, E, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	644	0.81	0.86	62	empty
2	187	0.81	0.95	38	empty
3	204	0.80	0.94	39	PLP
4	203	0.80	0.94	33	PLP
5	234	0.79	0.92	36	PLP

Interfaces

13 interfaces between chains.

B–H · 1430 Å² buried · 26 hydrogen bonds · protein-protein
F–A · 1425 Å² buried · 28 hydrogen bonds · protein-protein
C–G · 1420 Å² buried · 28 hydrogen bonds · protein-protein
D–E · 1417 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 601 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).

Compared structures

4H6D · Crystal structure of PLP-soaked HMP synthase Thi5 from S. cerevisiae · the same entry in another collection · chain H against H, TM-score 1.00
P43534 · AlphaFold monomer V2.0 prediction for 4-amino-5-hydroxymethyl-2-methylpyrimidine… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P43534
Elsewhere: RCSB PDB 4H6D · PDBe 4H6D · UniProt P43534

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