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Trypanosoma brucei PTR1 in complex with inhibitor 4G (F125)

Analyse Trypanosoma brucei PTR1 in complex with inhibitor 4G (F125) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GEY
Type: protein
Length: 1,005 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: NAP, EWT
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pteridine reductase	protein	252	46% helix, 14% strand	O76290
B	Pteridine reductase	protein	252	46% helix, 15% strand	O76290
C	Pteridine reductase	protein	251	47% helix, 15% strand	O76290
D	Pteridine reductase	protein	250	47% helix, 15% strand	O76290

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
EWT · 2-azanyl-~{N}-[(3,4-dichlorophenyl)methyl]-1,3-benzothiazole-6-carboxamide · ligand · 4 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, D
ACT · Acetate ion · additive · chains C

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.83	0.84	69	empty
2	634	0.77	0.83	48	NAP, EWT, DMS
3	614	0.77	0.83	49	NAP, EWT
4	628	0.76	0.82	50	NAP, EWT, DMS
5	573	0.74	0.81	47	NAP, EWT, DMS

Interfaces

6 interfaces between chains.

B–D · 1919 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1866 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1431 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1418 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 558 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6GEY · Trypanosoma brucei PTR1 in complex with inhibitor 4g (F125) · 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 O76290
Elsewhere: RCSB PDB 6GEY · PDBe 6GEY · UniProt O76290

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