MolNFT v1 · #110701 · protein

Crystal structure of yeast THI4-C205S

4Y4L · Thiamine thiazole synthase: “Crystal structure of yeast THI4-C205S”. X-ray diffraction, 1 ligand (48N), 10 pockets (best druggability 0.78). MolNFT v1 #110701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Y4L
Type: protein
Length: 1,202 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamine thiazole synthase
UniProt: P32318
Ligands: 48N
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Thiamine thiazole synthase	protein	303	33% helix, 22% strand	P32318
B	Thiamine thiazole synthase	protein	297	34% helix, 20% strand	P32318
C	Thiamine thiazole synthase	protein	299	34% helix, 21% strand	P32318

Ligands and binding sites

48N · (2E)-2-[(2S,4R)-5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-3-oxidanylidene-pentan-2-yl]iminoethanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	871	0.78	0.81	99	48N
2	890	0.77	0.80	92	48N
3	916	0.72	0.76	67	empty
4	70	0.48	0.83	16	empty
5	70	0.46	0.82	15	empty

Interfaces

3 interfaces between chains.

A–B · 4020 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 3933 Å² buried · 46 hydrogen bonds · protein-protein
B–D · 177 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4Y4L · Crystal structure of yeast Thi4-C205S · the same entry in another collection · chain A against A, TM-score 1.00
P32318 · AlphaFold monomer V2.0 prediction for thiamine thiazole synthase (P32318) · a predicted model of the same protein · 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 P32318
Elsewhere: RCSB PDB 4Y4L · PDBe 4Y4L · UniProt P32318

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