MolNFT v1 · #89530 · protein
The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from rhizobium meliloti
4DRY: “The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from rhizobium meliloti”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.84). MolNFT v1 #89530 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4DRY
- Type
- protein
- Length
- 985 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
- Q92TX5
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 241 | 47% helix, 22% strand | Q92TX5 |
| B, C, D | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 248 | 48% helix, 21% strand | Q92TX5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
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 | 1173 | 0.84 | 0.85 | 65 | empty |
| 2 | 622 | 0.70 | 0.78 | 64 | SO4 |
| 3 | 658 | 0.70 | 0.78 | 70 | SO4 |
| 4 | 490 | 0.69 | 0.79 | 55 | SO4 |
| 5 | 425 | 0.64 | 0.78 | 53 | SO4 |
Interfaces
6 interfaces between chains.
- A–D · 1751 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1736 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1468 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 620 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 4DRY · The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Rhizobium… · 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 Q92TX5
- Elsewhere: RCSB PDB 4DRY · PDBe 4DRY · UniProt Q92TX5
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