MolNFT v1 · #134493 · protein
Crystal structure of short-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase from brucella melitensis
5T5Q: “Crystal structure of short-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase from brucella…”. X-ray diffraction, 2 ligands (NAD, SO4), 7 pockets (best druggability 0.83). MolNFT v1 #134493 on GenesisL1: 3D structure…
- PDB
- 5T5Q
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase
- EC
- 1.1.1.100
- UniProt
- Q2YL80
- Ligands
- NAD, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase (EC 1.1.1.100) | protein | 237 | 49% helix, 19% strand | Q2YL80 |
| B | Short-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase (EC 1.1.1.100) | protein | 235 | 50% helix, 19% strand | Q2YL80 |
| C, D | Short-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase (EC 1.1.1.100) | protein | 245 | 52% helix, 18% strand | Q2YL80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.83 | 0.94 | 52 | SO4, MPD |
| 2 | 677 | 0.78 | 0.83 | 78 | NAD |
| 3 | 444 | 0.73 | 0.83 | 49 | NAD |
| 4 | 330 | 0.63 | 0.79 | 46 | NAD |
| 5 | 362 | 0.63 | 0.78 | 40 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 1727 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1722 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1689 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1673 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5T5Q · Crystal structure of Short-chain dehydrogenase/reductase SDR:Glucose/ribitol… · 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 Q2YL80
- Elsewhere: RCSB PDB 5T5Q · PDBe 5T5Q · UniProt Q2YL80
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