Research workbench
Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from brucella melitensis in complex with NAD
Analyse Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from brucella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VN2
- Type
- protein
- Length
- 1,018 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-(acyl-carrier protein) reductase
- EC
- 1.1.1.100
- UniProt
- Q8YJQ6
- Ligands
- NAD
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 3-oxoacyl-(acyl-carrier protein) reductase (EC 1.1.1.100) | protein | 253 | 47% helix, 17% strand | Q8YJQ6 |
| B | 3-oxoacyl-(acyl-carrier protein) reductase (EC 1.1.1.100) | protein | 255 | 47% helix, 16% strand | Q8YJQ6 |
| C | 3-oxoacyl-(acyl-carrier protein) reductase (EC 1.1.1.100) | protein | 257 | 46% helix, 16% strand | Q8YJQ6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.81 | 0.83 | 98 | empty |
| 2 | 357 | 0.78 | 0.88 | 46 | NAD, ACT |
| 3 | 325 | 0.74 | 0.86 | 42 | NAD, ACT |
| 4 | 341 | 0.74 | 0.86 | 44 | NAD, ACT |
| 5 | 307 | 0.71 | 0.84 | 41 | NAD, ACT |
Interfaces
6 interfaces between chains.
- A–C · 1572 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1559 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1448 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1441 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5VN2 · Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis… · 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 Q8YJQ6
- Elsewhere: RCSB PDB 5VN2 · PDBe 5VN2 · UniProt Q8YJQ6
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