MolNFT v1 · #136571 · protein
Structure of proline utilization a (puta) from corynebacterium freiburgense
5UX5 · Bifunctional protein proline utilization a (puta): “Structure of proline utilization a (puta) from corynebacterium freiburgense”. X-ray diffraction, 3 ligands (FAD, NAD, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #136571…
- PDB
- 5UX5
- Type
- protein
- Length
- 3,849 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein proline utilization a (puta)
- EC
- 1.5.5.22, 1.2.1.88
- Ligands
- FAD, NAD, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein proline utilization a (puta) (EC 1.5.5.22, 1.2.1.88) | protein | 963 | 45% helix, 18% strand | — |
| B, C, D | Bifunctional protein proline utilization a (puta) (EC 1.5.5.22, 1.2.1.88) | protein | 962 | 45% helix, 18% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.86 | 0.89 | 119 | SO4 |
| 2 | 549 | 0.86 | 0.92 | 62 | empty |
| 3 | 693 | 0.85 | 0.88 | 66 | empty |
| 4 | 310 | 0.83 | 0.93 | 64 | SO4 |
| 5 | 280 | 0.82 | 0.94 | 60 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1133 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1100 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5UX5 · Structure of Proline Utilization A (PutA) from Corynebacterium freiburgense · 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 5UX5 · PDBe 5UX5
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