Research workbench
Crystal structure of human sepiapterin reductase in complex with an N- acetylserotinin analogue
Analyse Crystal structure of human sepiapterin reductase in complex with an N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XWY
- Type
- protein
- Length
- 1,028 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
- NDP, 43O, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sepiapterin reductase (EC 1.1.1.153) | protein | 257 | 49% helix, 18% strand | P35270 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 43O · N-[2-(5-hydroxy-2-methyl-1H-indol-3-yl)ethyl]-2-methoxyacetamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.76 | 0.84 | 54 | NDP, 43O |
| 2 | 483 | 0.76 | 0.84 | 50 | NDP, 43O |
| 3 | 499 | 0.76 | 0.84 | 48 | NDP, 43O |
| 4 | 500 | 0.76 | 0.84 | 54 | NDP, 43O |
| 5 | 1020 | 0.76 | 0.78 | 84 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1990 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1955 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 255 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4XWY · Crystal structure of human sepiapterin reductase in complex with an N-acetylserotinin… · 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 4XWY · PDBe 4XWY · UniProt P35270
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