MolNFT v1 · #95562 · protein
Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S- hpcdh) bound to S-hpc and NADH
4ITU · Short-chain DEHYDROGENASE/REDUCTASE sdr: “Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S- hpcdh) bound to S-hpc and NADH”. X-ray diffraction, 2 ligands (NAI, 1HS), 9 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 4ITU
- Type
- protein
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A7IQH5
- Ligands
- NAI, 1HS
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 253 | 50% helix, 17% strand | A7IQH5 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 250 | 50% helix, 17% strand | A7IQH5 |
| C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 246 | 50% helix, 17% strand | A7IQH5 |
| D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 249 | 51% helix, 17% strand | A7IQH5 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 1HS · 2-{[(2S)-2-hydroxypropyl]sulfanyl}ethanesulfonic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.85 | 0.87 | 67 | empty |
| 2 | 1166 | 0.82 | 0.83 | 115 | NAI, 1HS |
| 3 | 1146 | 0.82 | 0.83 | 119 | NAI, 1HS |
| 4 | 82 | 0.42 | 0.79 | 14 | empty |
| 5 | 60 | 0.37 | 0.79 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1419 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1374 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1364 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4ITU · Crystal structure of S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (S-HPCDH) bound to S-HPC… · 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 A7IQH5
- Elsewhere: RCSB PDB 4ITU · PDBe 4ITU · UniProt A7IQH5
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