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Structure of escherichia COLI bound to dgtp

Analyse Structure of escherichia COLI bound to dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OIY
Type: protein
Length: 2,985 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyguanosinetriphosphate triphosphohydrolase
EC: 3.1.5.1
UniProt: P15723
Ligands: DGT, MN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 61% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1)	protein	503	60% helix, 1% strand	P15723
D, E, F	Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1)	protein	492	62% helix, 2% strand	P15723

Ligands and binding sites

DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, F, E
MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1019	0.81	0.82	95	empty
2	1039	0.81	0.82	94	empty
3	987	0.80	0.81	91	empty
4	872	0.78	0.81	84	empty
5	655	0.75	0.81	69	empty

Interfaces

12 interfaces between chains.

B–D · 2101 Å² buried · 31 hydrogen bonds · protein-protein
C–E · 2037 Å² buried · 26 hydrogen bonds · protein-protein
A–F · 2033 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 763 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 737 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6OIY · Structure of Escherichia coli bound to dGTP · the same entry in another collection · chain F against F, TM-score 1.00
P15723 · AlphaFold monomer V2.0 prediction for deoxyguanosinetriphosphate triphosphohydrolase… · a predicted model of the same protein · chain D 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 P15723
Elsewhere: RCSB PDB 6OIY · PDBe 6OIY · UniProt P15723

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