MolNFT v1 · #65098 · protein

Structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (DDD00066730)

3GN2: “Structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+)…”. X-ray diffraction, 2 ligands (AX8, NAP), 10 pockets (best druggability 0.85). MolNFT v1 #65098 on GenesisL1: 3D structure…

PDB: 3GN2
Type: protein
Length: 994 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: AX8, NAP
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Pteridine reductase	protein	249	48% helix, 14% strand	O76290
B	Pteridine reductase	protein	248	48% helix, 14% strand	O76290
C	Pteridine reductase	protein	248	48% helix, 14% strand	O76290

Ligands and binding sites

AX8 · 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine · ligand · 5 copies · chains A, D, B, C
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · chains A

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

Pockets

10 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	899	0.85	0.86	71	empty
2	750	0.80	0.83	50	NAP, AX8
3	735	0.78	0.82	51	NAP, AX8
4	690	0.76	0.81	51	NAP, AX8
5	671	0.75	0.80	48	NAP, AX8

Interfaces

6 interfaces between chains.

B–D · 1877 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1861 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1407 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1388 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 577 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3GN2 · Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with… · 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 3GN2 · PDBe 3GN2 · UniProt O76290

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