Research workbench
Crystal structure of phab from ralstonia eutropha in complex with acetoacetyl-CoA and NADP
Analyse Crystal structure of phab from ralstonia eutropha in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZS
- Type
- protein
- Length
- 986 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
- P14697
- Ligands
- NAP, CAA, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acetoacetyl-CoA reductase (EC 1.1.1.36) | protein | 244 | 50% helix, 16% strand | P14697 |
| B, D | Acetoacetyl-CoA reductase (EC 1.1.1.36) | protein | 249 | 48% helix, 16% strand | P14697 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- CAA · Acetoacetyl-coenzyme A · ligand · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.86 | 0.90 | 72 | empty |
| 2 | 944 | 0.79 | 0.81 | 89 | SO4, NAP, CAA |
| 3 | 444 | 0.72 | 0.82 | 58 | NAP |
| 4 | 502 | 0.70 | 0.80 | 59 | SO4, NAP |
| 5 | 505 | 0.70 | 0.80 | 61 | SO4, NAP |
Interfaces
6 interfaces between chains.
- A–D · 1782 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1702 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1420 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1414 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 163 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3VZS · Crystal structure of PhaB from Ralstonia eutropha in complex with Acetoacetyl-CoA and NADP · the same entry in another collection · chain A against A, TM-score 1.00
- P14697 · AlphaFold monomer V2.0 prediction for acetoacetyl-CoA reductase (P14697) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P14697
- Elsewhere: RCSB PDB 3VZS · PDBe 3VZS · UniProt P14697
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