Research workbench
Structure of proline utilization a from sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21
Analyse Structure of proline utilization a from sinorhizobium meliloti complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KF6
- Type
- protein
- Length
- 2,407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- UniProt
- F7X6I3
- Ligands
- FAD, NAD, TFB, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta | protein | 1207 | 49% helix, 14% strand | F7X6I3 |
| B | Bifunctional protein puta | protein | 1200 | 49% helix, 15% strand | F7X6I3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- TFB · Tetrahydrofuran-2-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 8 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.86 | 0.90 | 86 | FAD, TFB, PGE |
| 2 | 834 | 0.85 | 0.88 | 134 | NAD, PGE |
| 3 | 751 | 0.85 | 0.88 | 120 | NAD, PGE |
| 4 | 1179 | 0.83 | 0.84 | 95 | FAD, TFB |
| 5 | 986 | 0.79 | 0.81 | 100 | empty |
Interfaces
1 interface between chains.
- A–B · 1906 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5KF6 · Structure of proline utilization A from Sinorhizobium meliloti complexed with… · 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 F7X6I3
- Elsewhere: RCSB PDB 5KF6 · PDBe 5KF6 · UniProt F7X6I3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.