MolNFT v1 · #62778 · protein

Crystal structure of caulobacter crescentus thic

3EPM · Thiamine biosynthesis protein thic: “Crystal structure of caulobacter crescentus thic”. X-ray diffraction, 3 ligands (HMH, ZN, SO4), 14 pockets (best druggability 0.76). MolNFT v1 #62778 on GenesisL1: 3D structure, binding sites and…

PDB: 3EPM
Type: protein
Length: 1,027 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamine biosynthesis protein thic
UniProt: Q9A6Q5
Ligands: HMH, ZN, SO4
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiamine biosynthesis protein thic	protein	515	42% helix, 11% strand	Q9A6Q5
B	Thiamine biosynthesis protein thic	protein	512	41% helix, 12% strand	Q9A6Q5

Ligands and binding sites

HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains A

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.76	0.98	19	empty
2	662	0.73	0.80	54	ZN
3	622	0.72	0.79	52	ZN, HMH
4	154	0.66	0.87	31	empty
5	304	0.56	0.76	26	empty

Interfaces

1 interface between chains.

A–B · 2647 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

3EPM · Crystal structure of Caulobacter crescentus ThiC · the same entry in another collection · chain A against A, TM-score 1.00
Q9A6Q5 · AlphaFold monomer V2.0 prediction for phosphomethylpyrimidine synthase (Q9A6Q5) · a predicted model of the same protein · chain B 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 Q9A6Q5
Elsewhere: RCSB PDB 3EPM · PDBe 3EPM · UniProt Q9A6Q5

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