MolNFT v1 · #150567 · protein

Tryparedoxin from trypanosoma brucei in complex with cft

6GXG: “Tryparedoxin from trypanosoma brucei in complex with cft”. X-ray diffraction, 1 ligand (FFN), 4 pockets (best druggability 0.71). MolNFT v1 #150567 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GXG
Type: protein
Length: 438 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryparedoxin
UniProt: O77404
Ligands: FFN
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tryparedoxin	protein	144	35% helix, 21% strand	O77404
B, C	Tryparedoxin	protein	147	37% helix, 22% strand	O77404

Ligands and binding sites

FFN · 5-(4-fluorophenyl)-2-methyl-3~{H}-thieno[2,3-d]pyrimidin-4-one · ligand · 3 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.71	0.81	33	FFN
2	324	0.57	0.76	30	empty
3	118	0.50	0.81	17	empty
4	164	0.42	0.74	25	GOL

Interfaces

2 interfaces between chains.

A–B · 336 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 333 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6GXG · Tryparedoxin from Trypanosoma brucei in complex with CFT · the same entry in another collection · chain A against A, TM-score 1.00
O77404 · AlphaFold monomer V2.0 prediction for tryparedoxin (O77404) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O77404
Elsewhere: RCSB PDB 6GXG · PDBe 6GXG · UniProt O77404

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