MolNFT v1 · #137585 · protein
Crystal structure of acetoacetyl-CoA reductase from burkholderia pseudomallei 1710B complexed with NADP
5VT6: “Crystal structure of acetoacetyl-CoA reductase from burkholderia pseudomallei 1710B complexed with NADP”. X-ray diffraction, 1 ligand (NAP), 10 pockets (best druggability 0.85). MolNFT v1 #137585 on GenesisL1: 3D structure, binding…
- PDB
- 5VT6
- Type
- protein
- Length
- 956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetyl-CoA reductase
- EC
- 1.1.1.36
- UniProt
- Q3JJT1
- Ligands
- NAP
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetoacetyl-CoA reductase (EC 1.1.1.36) | protein | 245 | 48% helix, 16% strand | Q3JJT1 |
| B | Acetoacetyl-CoA reductase (EC 1.1.1.36) | protein | 237 | 47% helix, 17% strand | Q3JJT1 |
| C | Acetoacetyl-CoA reductase (EC 1.1.1.36) | protein | 240 | 47% helix, 17% strand | Q3JJT1 |
| D | Acetoacetyl-CoA reductase (EC 1.1.1.36) | protein | 234 | 44% helix, 17% strand | Q3JJT1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
- IMD · Imidazole · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.85 | 0.89 | 84 | empty |
| 2 | 493 | 0.67 | 0.78 | 49 | NAP, ACT, EDO |
| 3 | 432 | 0.63 | 0.77 | 37 | empty |
| 4 | 374 | 0.61 | 0.77 | 40 | NAP, ACT, EDO |
| 5 | 366 | 0.60 | 0.77 | 31 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1674 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1652 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1512 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1509 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 191 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VT6 · Crystal structure of Acetoacetyl-CoA Reductase from Burkholderia pseudomallei 1710b… · 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 Q3JJT1
- Elsewhere: RCSB PDB 5VT6 · PDBe 5VT6 · UniProt Q3JJT1
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