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The X-ray crystal structure of streptococcus pneumoniae fatty acid kinase (fak) B2 protein loaded with vaccenic acid (C18:1 DELTA11) to 2.1 ångström resolution
Analyse The X-ray crystal structure of streptococcus pneumoniae fatty acid kinase (fak)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NR1
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid kinase (fak) B2 protein (SPR1019)
- UniProt
- A0A0I9AIE4
- Ligands
- VCA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty acid kinase (fak) B2 protein (SPR1019) | protein | 279 | 41% helix, 26% strand | A0A0I9AIE4 |
| B | Fatty acid kinase (fak) B2 protein (SPR1019) | protein | 278 | 40% helix, 26% strand | A0A0I9AIE4 |
Ligands and binding sites
- VCA · Vaccenic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.80 | 0.96 | 33 | VCA |
| 2 | 155 | 0.79 | 0.96 | 31 | VCA |
| 3 | 541 | 0.74 | 0.82 | 39 | empty |
| 4 | 265 | 0.60 | 0.79 | 34 | empty |
| 5 | 175 | 0.55 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 849 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6NR1 · The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2… · 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 A0A0I9AIE4
- Elsewhere: RCSB PDB 6NR1 · PDBe 6NR1 · UniProt A0A0I9AIE4
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