MolNFT v1 · #75252 · protein

Q83D variant of S. enterica rmla with dgtp

3PKQ · Glucose-1-phosphate thymidylyltransferase: “Q83D variant of S. enterica rmla with dgtp”. X-ray diffraction, 2 ligands (DGT, MG), 16 pockets (best druggability 0.75). MolNFT v1 #75252 on GenesisL1: 3D structure, binding sites and…

PDB: 3PKQ
Type: protein
Length: 1,133 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-1-phosphate thymidylyltransferase
EC: 2.7.7.24
UniProt: P26393
Ligands: DGT, MG
Pockets: 16 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)	protein	285	36% helix, 24% strand	P26393
B	Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)	protein	286	36% helix, 24% strand	P26393
C	Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)	protein	284	36% helix, 25% strand	P26393
D	Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)	protein	278	37% helix, 24% strand	P26393

Ligands and binding sites

DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 5 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.75	0.81	36	empty
2	991	0.75	0.78	88	DGT, MG
3	986	0.75	0.78	88	DGT, MG
4	57	0.74	0.99	14	PEG
5	972	0.73	0.77	84	DGT, MG

Interfaces

4 interfaces between chains.

C–D · 1636 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1631 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 895 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 805 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3PKQ · Q83D Variant of S. Enterica RmlA with dGTP · the same entry in another collection · chain D against D, TM-score 1.00
P26393 · AlphaFold monomer V2.0 prediction for glucose-1-phosphate thymidylyltransferase (P26393) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P26393
Elsewhere: RCSB PDB 3PKQ · PDBe 3PKQ · UniProt P26393

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