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Crystal structure of hmp synthase THI5 from S. cerevisiae

Analyse Crystal structure of 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: 4H67
Type: protein
Length: 2,588 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, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrimidine precursor biosynthesis enzyme THI5	protein	337	45% helix, 16% strand	P43534
B	Pyrimidine precursor biosynthesis enzyme THI5	protein	307	44% helix, 18% strand	P43534
C	Pyrimidine precursor biosynthesis enzyme THI5	protein	338	45% helix, 16% strand	P43534
D, F	Pyrimidine precursor biosynthesis enzyme THI5	protein	335	47% helix, 16% strand	P43534
E	Pyrimidine precursor biosynthesis enzyme THI5	protein	305	44% helix, 18% strand	P43534
G	Pyrimidine precursor biosynthesis enzyme THI5	protein	326	48% helix, 17% strand	P43534
H	Pyrimidine precursor biosynthesis enzyme THI5	protein	305	43% helix, 18% strand	P43534

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains B
SO4 · Sulfate ion · ion · 17 copies · chains A, C, D, E, F, G, 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	975	0.83	0.84	100	SO4
2	1057	0.83	0.84	114	SO4
3	218	0.82	0.95	36	SO4
4	199	0.81	0.95	36	SO4
5	208	0.81	0.94	37	SO4

Interfaces

12 interfaces between chains.

C–E · 1380 Å² buried · 31 hydrogen bonds · protein-protein
D–H · 1340 Å² buried · 32 hydrogen bonds · protein-protein
F–G · 1334 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1330 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 332 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

4H67 · Crystal structure of 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 H 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 4H67 · PDBe 4H67 · UniProt P43534

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