MolNFT v1 · #124134 · protein

Trypanosoma brucei pteridine reductase 1 (PTR1) in complex with compound 1

5K6A: “Trypanosoma brucei pteridine reductase 1 (PTR1) in complex with compound 1”. X-ray diffraction, 2 ligands (NAP, 6QT), 7 pockets (best druggability 0.83). MolNFT v1 #124134 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5K6A
Type: protein
Length: 981 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pteridine reductase
UniProt: O76290
Ligands: NAP, 6QT
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Pteridine reductase	protein	248	47% helix, 15% strand	O76290
B	Pteridine reductase	protein	247	48% helix, 15% strand	O76290
C	Pteridine reductase	protein	238	47% helix, 16% strand	O76290

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
6QT · (2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one · ligand · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · 2 copies · chains A, C

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

Pockets

7 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	1179	0.83	0.84	72	empty
2	603	0.76	0.82	49	NAP, 6QT
3	585	0.76	0.82	48	NAP, 6QT
4	599	0.75	0.82	48	NAP, 6QT
5	490	0.67	0.78	44	NAP, 6QT

Interfaces

6 interfaces between chains.

B–D · 1864 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1831 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1438 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1412 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 566 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (oxidation).

Compared structures

5K6A · Trypanosoma brucei Pteridine reductase 1 (PTR1) in complex with compound 1 · 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 5K6A · PDBe 5K6A · UniProt O76290

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