Research workbench
Crystal structure of pdua with edge mutation K26A and pore mutation S40H
Analyse Crystal structure of pdua with edge mutation K26A and pore mutation S40H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QIF
- Type
- protein
- Length
- 791 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propanediol utilization protein pdua
- UniProt
- P0A1C7
- Ligands
- K, SO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Propanediol utilization protein pdua | protein | 91 | 30% helix, 41% strand | P0A1C7 |
| B | Propanediol utilization protein pdua | protein | 86 | 36% helix, 40% strand | P0A1C7 |
| C | Propanediol utilization protein pdua | protein | 90 | 38% helix, 38% strand | P0A1C7 |
| D | Propanediol utilization protein pdua | protein | 88 | 34% helix, 39% strand | P0A1C7 |
| E | Propanediol utilization protein pdua | protein | 86 | 34% helix, 40% strand | P0A1C7 |
| F | Propanediol utilization protein pdua | protein | 91 | 37% helix, 36% strand | P0A1C7 |
| G, I | Propanediol utilization protein pdua | protein | 84 | 40% helix, 37% strand | P0A1C7 |
| H | Propanediol utilization protein pdua | protein | 91 | 35% helix, 37% strand | P0A1C7 |
Ligands and binding sites
- K · Potassium ion · metal
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, D, F, C, E, G, H, I
- GOL · Glycerol · additive · 8 copies · chains B, D, E, A, C, F, G, H
- PGO · S-1,2-propanediol · additive · 3 copies · chains A, B, F, C, D, E, G, I
- TAR · D(-)-tartaric acid · additive · 3 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.59 | 0.78 | 25 | PGO, SO4, TAR |
| 2 | 136 | 0.49 | 0.79 | 25 | PGO |
| 3 | 74 | 0.39 | 0.78 | 21 | SO4 |
| 4 | 70 | 0.37 | 0.77 | 18 | empty |
| 5 | 66 | 0.33 | 0.76 | 16 | empty |
Interfaces
10 interfaces between chains.
- B–D · 957 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 944 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 850 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 841 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 821 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4QIF · Crystal Structure of PduA with edge mutation K26A and pore mutation S40H · the same entry in another collection · chain I against I, TM-score 1.00
- P0A1C7 · AlphaFold monomer V2.0 prediction for propanediol utilization protein pdua (P0A1C7) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 4QIF · PDBe 4QIF · UniProt P0A1C7
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