Research workbench
Short-chain dehydrogenase from sphingobium yanoikuyae in complex with NADPH
Analyse Short-chain dehydrogenase from sphingobium yanoikuyae in complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BMV
- Type
- protein
- Length
- 2,562 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain dehydrogenase
- EC
- 1.1.1.1
- UniProt
- B9U359
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain dehydrogenase (EC 1.1.1.1) | protein | 256 | 54% helix, 14% strand | B9U359 |
| B, D, E | Short-chain dehydrogenase (EC 1.1.1.1) | protein | 257 | 55% helix, 14% strand | B9U359 |
| C | Short-chain dehydrogenase (EC 1.1.1.1) | protein | 258 | 55% helix, 14% strand | B9U359 |
| F, G, H | Short-chain dehydrogenase (EC 1.1.1.1) | protein | 256 | 55% helix, 15% strand | B9U359 |
| I | Short-chain dehydrogenase (EC 1.1.1.1) | protein | 254 | 53% helix, 15% strand | B9U359 |
| J | Short-chain dehydrogenase (EC 1.1.1.1) | protein | 255 | 54% helix, 15% strand | B9U359 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.85 | 0.87 | 113 | NAP |
| 2 | 794 | 0.85 | 0.87 | 103 | NAP |
| 3 | 192 | 0.84 | 0.98 | 26 | empty |
| 4 | 196 | 0.84 | 0.98 | 28 | empty |
| 5 | 192 | 0.84 | 0.97 | 23 | empty |
Interfaces
9 interfaces between chains.
- E–F · 3849 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3818 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3793 Ų buried · 48 hydrogen bonds · protein-protein
- G–J · 3687 Ų buried · 46 hydrogen bonds · protein-protein
- H–I · 3539 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 4BMV · Short-chain dehydrogenase from Sphingobium yanoikuyae in complex with NADPH · the same entry in another collection · chain J against J, 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 B9U359
- Elsewhere: RCSB PDB 4BMV · PDBe 4BMV · UniProt B9U359
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.