MolNFT v1 · #186620 · protein

Crystal structure of thermovibrio ammonificans THI4

7RK0 · Thiamine thiazole synthase: “Crystal structure of thermovibrio ammonificans THI4”. X-ray diffraction, 2 ligands (48H, FE), 10 pockets (best druggability 0.71). MolNFT v1 #186620 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7RK0
Type: protein
Length: 1,043 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamine thiazole synthase
EC: 2.4.2.59
UniProt: E8T346
Ligands: 48H, FE
Pockets: 10 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiamine thiazole synthase (EC 2.4.2.59)	protein	261	42% helix, 27% strand	E8T346
B, D	Thiamine thiazole synthase (EC 2.4.2.59)	protein	262	42% helix, 27% strand	E8T346
C	Thiamine thiazole synthase (EC 2.4.2.59)	protein	258	43% helix, 28% strand	E8T346

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 · 4 copies · chains A, B, C, D
FE · Fe (III) ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	420	0.71	0.82	54	FE, 48H
2	407	0.71	0.82	57	48H
3	548	0.68	0.78	55	FE, 48H
4	527	0.68	0.78	68	FE, 48H
5	59	0.46	0.83	14	empty

Interfaces

6 interfaces between chains.

B–C · 2670 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2638 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 1168 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1049 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1037 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7RK0 · Crystal structure of Thermovibrio ammonificans THI4 · 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
Every structure of UniProt E8T346
Elsewhere: RCSB PDB 7RK0 · PDBe 7RK0 · UniProt E8T346

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