MolNFT v1 · #110703 · protein

Thiazole synthase THI4 from methanococcus igneus

4Y4N · Putative ribose 1,5-bisphosphate isomerase: “Thiazole synthase THI4 from methanococcus igneus”. X-ray diffraction, 2 ligands (48H, FE2), 17 pockets (best druggability 0.85). MolNFT v1 #110703 on GenesisL1: 3D structure, binding…

PDB: 4Y4N
Type: protein
Length: 2,072 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ribose 1,5-bisphosphate isomerase
EC: 5.3.1.29
UniProt: F6BCS4
Ligands: 48H, FE2
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Putative ribose 1,5-bisphosphate isomerase (EC 5.3.1.29)	protein	259	41% helix, 28% strand	F6BCS4

Ligands and binding sites

48H · 2-[(E)-[(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-ylidene]amino]ethanoic acid · ligand · 8 copies · chains A, C, H, B, D, G, F, E
FE2 · Fe (II) ion · metal · 8 copies · chains A, C, H, B, D, G, F, E

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	253	0.85	0.96	43	empty
2	250	0.84	0.96	44	empty
3	242	0.84	0.95	42	empty
4	247	0.83	0.95	43	empty
5	1060	0.82	0.83	111	48H

Interfaces

20 interfaces between chains.

E–H · 2559 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 2551 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 2528 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 2514 Å² buried · 14 hydrogen bonds · protein-protein
B–F · 1304 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4Y4N · Thiazole synthase Thi4 from Methanococcus igneus · the same entry in another collection · chain F against F, TM-score 1.00
F6BCS4 · AlphaFold monomer V2.0 prediction for thiamine thiazole synthase (F6BCS4) · 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 F6BCS4
Elsewhere: RCSB PDB 4Y4N · PDBe 4Y4N · UniProt F6BCS4

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