Research workbench
Chlorobium tepidum sepiapterin reductase complexed with NADP and sepiapterin
Analyse Chlorobium tepidum sepiapterin reductase complexed with NADP and sepiapterin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BD0
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sepiapterin reductase
- EC
- 1.1.1.153
- UniProt
- Q8KES3
- Ligands
- NAP, BIO
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sepiapterin reductase (EC 1.1.1.153) | protein | 240 | 46% helix, 20% strand | Q8KES3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- BIO · Biopterin · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.78 | 0.80 | 79 | empty |
| 2 | 432 | 0.76 | 0.85 | 45 | NAP |
| 3 | 439 | 0.76 | 0.85 | 47 | NAP |
| 4 | 429 | 0.75 | 0.84 | 48 | NAP |
| 5 | 454 | 0.74 | 0.83 | 46 | NAP, BIO |
Interfaces
4 interfaces between chains.
- A–B · 1632 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1630 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1151 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1130 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2BD0 · Chlorobium tepidum Sepiapterin Reductase complexed with NADP and Sepiapterin · the same entry in another collection · chain A against A, TM-score 1.00
- Q8KES3 · AlphaFold monomer V2.0 prediction for sepiapterin reductase (Q8KES3) · a predicted model of the same protein · 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 Q8KES3
- Elsewhere: RCSB PDB 2BD0 · PDBe 2BD0 · UniProt Q8KES3
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