Research workbench
Structure of proline utilization a from sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P3121
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
- 5KF7
- Type
- protein
- Length
- 1,211 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- UniProt
- F7X6I3
- Ligands
- FAD, NAD, TFB, MG, SO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta | protein | 1211 | 48% helix, 15% strand | F7X6I3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- TFB · Tetrahydrofuran-2-carboxylic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.87 | 0.90 | 91 | FAD, TFB |
| 2 | 545 | 0.82 | 0.88 | 84 | PG4 |
| 3 | 62 | 0.71 | 0.97 | 16 | empty |
| 4 | 385 | 0.69 | 0.81 | 58 | empty |
| 5 | 396 | 0.64 | 0.78 | 43 | NAD, MG |
Compared structures
- 5KF7 · 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 5KF7 · PDBe 5KF7 · UniProt F7X6I3
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