Research workbench

Co-crystal structure of spr with compound 5

Analyse Co-crystal structure of spr with compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6USN
Type: protein
Length: 1,032 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sepiapterin reductase
EC: 1.1.1.153
UniProt: P35270
Ligands: NAP, QGV, SO4
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Sepiapterin reductase (EC 1.1.1.153)	protein	258	48% helix, 17% strand	P35270

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
QGV · (2-hydroxyphenyl)[3-methyl-1-(pyridin-2-yl)-1H-pyrazolo[3,4-b]pyridin-5-yl]methanone · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
GOL · Glycerol · additive · 5 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	540	0.77	0.84	61	NAP, QGV
2	489	0.77	0.84	52	NAP, PEG, QGV
3	541	0.76	0.83	58	NAP, QGV
4	509	0.75	0.83	56	NAP, PEG, QGV
5	79	0.36	0.77	17	empty

Interfaces

3 interfaces between chains.

B–D · 1962 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1941 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 392 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6USN · Co-crystal structure of SPR with compound 5 · the same entry in another collection · chain A against A, TM-score 1.00
P35270 · AlphaFold monomer V2.0 prediction for sepiapterin reductase (P35270) · a predicted model of the same protein · chain A 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 P35270
Elsewhere: RCSB PDB 6USN · PDBe 6USN · UniProt P35270

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.