Research workbench
Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S- hpcdh)
Analyse Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S- hpcdh) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GH5
- Type
- protein
- Length
- 985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A7IQH5
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 248 | 50% helix, 17% strand | A7IQH5 |
| B, D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 245 | 49% helix, 17% strand | A7IQH5 |
| C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 247 | 50% helix, 17% strand | A7IQH5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.85 | 0.87 | 71 | empty |
| 2 | 615 | 0.79 | 0.84 | 69 | NAD, ACT |
| 3 | 705 | 0.78 | 0.82 | 67 | NAD, ACT |
| 4 | 483 | 0.77 | 0.85 | 53 | NAD, ACT |
| 5 | 524 | 0.76 | 0.83 | 58 | NAD, ACT |
Interfaces
6 interfaces between chains.
- C–D · 1416 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1416 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1368 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1368 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GH5 · Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S-HPCDH) · 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 4GH5 · PDBe 4GH5 · UniProt A7IQH5
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