MolNFT v1 · #174360 · protein
Sdr protein napw-NADP
7BSX · Short chain dehydrogenase: “Sdr protein napw-NADP”. X-ray diffraction, 1 ligand (NAP), 20 pockets (best druggability 0.79). MolNFT v1 #174360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BSX
- Type
- protein
- Length
- 2,427 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- S4TKM8
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short chain dehydrogenase | protein | 305 | 48% helix, 12% strand | S4TKM8 |
| B, C, D, E, G, H | Short chain dehydrogenase | protein | 303 | 49% helix, 12% strand | S4TKM8 |
| F | Short chain dehydrogenase | protein | 304 | 48% helix, 12% strand | S4TKM8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.79 | 0.83 | 91 | NAP |
| 2 | 561 | 0.78 | 0.84 | 67 | NAP |
| 3 | 542 | 0.78 | 0.85 | 49 | NAP |
| 4 | 584 | 0.78 | 0.84 | 61 | NAP |
| 5 | 570 | 0.78 | 0.84 | 53 | NAP |
Interfaces
10 interfaces between chains.
- A–E · 1794 Ų buried · 30 hydrogen bonds · protein-protein
- C–G · 1790 Ų buried · 29 hydrogen bonds · protein-protein
- C–H · 514 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 514 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7BSX · SDR protein NapW-NADP · 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 S4TKM8
- Elsewhere: RCSB PDB 7BSX · PDBe 7BSX · UniProt S4TKM8
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