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Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from brucella melitensis complexed with NADH
Analyse Crystal structure of 3-ketoacyl-(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
- 6B9U
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase, subunit B:SHORT-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL…
- UniProt
- Q2YJS1
- Ligands
- NAI
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase, subunit B:SHORT-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase | protein | 244 | 50% helix, 16% strand | Q2YJS1 |
| B | DNA gyrase, subunit B:SHORT-chain DEHYDROGENASE/REDUCTASE SDR:GLUCOSE/RIBITOL dehydrogenase | protein | 242 | 50% helix, 17% strand | Q2YJS1 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.76 | 0.85 | 49 | NAI |
| 2 | 465 | 0.73 | 0.83 | 51 | NAI |
| 3 | 287 | 0.56 | 0.76 | 39 | empty |
| 4 | 115 | 0.45 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6B9U · Crystal structure of 3-ketoacyl-(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 Q2YJS1
- Elsewhere: RCSB PDB 6B9U · PDBe 6B9U · UniProt Q2YJS1
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