Research workbench
Crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from mycobacterium smegmatis with bound NAD
Analyse Crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CXA
- Type
- protein
- Length
- 997 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] reductase
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-oxoacyl-[acyl-carrier-protein] reductase | protein | 251 | 49% helix, 16% strand | — |
| D | 3-oxoacyl-[acyl-carrier-protein] reductase | protein | 244 | 51% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.86 | 0.89 | 76 | empty |
| 2 | 511 | 0.79 | 0.86 | 71 | NAD |
| 3 | 474 | 0.79 | 0.86 | 57 | NAD |
| 4 | 173 | 0.59 | 0.82 | 27 | empty |
| 5 | 242 | 0.58 | 0.79 | 31 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1711 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1645 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1523 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1518 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 302 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 8CXA · Crystal Structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium… · 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
- Elsewhere: RCSB PDB 8CXA · PDBe 8CXA
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