MolNFT v1 · #109906 · protein
Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from burkholderia thailandensis
4XGN: “Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from burkholderia thailandensis”. X-ray diffraction, 1 ligand (NAD), 18 pockets (best druggability 0.86). MolNFT v1 #109906 on GenesisL1: 3D structure, binding…
- PDB
- 4XGN
- Type
- protein
- Length
- 2,037 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase
- UniProt
- Q2T0K5
- Ligands
- NAD
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, H | 3-hydroxyacyl-CoA dehydrogenase | protein | 255 | 45% helix, 18% strand | Q2T0K5 |
| D | 3-hydroxyacyl-CoA dehydrogenase | protein | 254 | 46% helix, 18% strand | Q2T0K5 |
| E | 3-hydroxyacyl-CoA dehydrogenase | protein | 253 | 46% helix, 18% strand | Q2T0K5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 4 copies · chains B, C, A, D, F, G, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.86 | 0.87 | 79 | EDO, GOL |
| 2 | 1160 | 0.85 | 0.86 | 69 | GOL |
| 3 | 353 | 0.73 | 0.84 | 43 | NAD, EDO |
| 4 | 427 | 0.72 | 0.82 | 50 | NAD, EDO |
| 5 | 419 | 0.72 | 0.82 | 49 | NAD, EDO |
Interfaces
15 interfaces between chains.
- A–C · 1752 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 1746 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1728 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 1712 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1594 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4XGN · Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from… · the same entry in another collection · chain H against H, 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 Q2T0K5
- Elsewhere: RCSB PDB 4XGN · PDBe 4XGN · UniProt Q2T0K5
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