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Crystal structure of pdua with edge mutation K26D
Analyse Crystal structure of pdua with edge mutation K26D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QIE
- Type
- protein
- Length
- 779 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propanediol utilization protein pdua
- UniProt
- P0A1C7
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Propanediol utilization protein pdua | protein | 88 | 32% helix, 43% strand | P0A1C7 |
| B | Propanediol utilization protein pdua | protein | 87 | 37% helix, 36% strand | P0A1C7 |
| C, I | Propanediol utilization protein pdua | protein | 85 | 39% helix, 36% strand | P0A1C7 |
| E | Propanediol utilization protein pdua | protein | 86 | 37% helix, 37% strand | P0A1C7 |
| G | Propanediol utilization protein pdua | protein | 83 | 40% helix, 40% strand | P0A1C7 |
| H | Propanediol utilization protein pdua | protein | 89 | 36% helix, 39% strand | P0A1C7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, D, H
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.46 | 0.75 | 24 | GOL |
| 2 | 60 | 0.41 | 0.82 | 20 | empty |
| 3 | 70 | 0.35 | 0.77 | 19 | empty |
| 4 | 59 | 0.27 | 0.73 | 17 | empty |
Interfaces
10 interfaces between chains.
- B–D · 930 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 918 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 912 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 900 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 875 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 P0A1C7
- Elsewhere: RCSB PDB 4QIE · PDBe 4QIE · UniProt P0A1C7
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