MolNFT v1 · #104698 · protein
Crystal structure of pdua with edge mutation K26A and pore mutation S40C
4QIG · Propanediol utilization protein pdua: “Crystal structure of pdua with edge mutation K26A and pore mutation S40C”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.69). MolNFT v1 #104698 on GenesisL1: 3D structure…
- PDB
- 4QIG
- Type
- protein
- Length
- 611 residues
- Chains
- 7
- 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 0.69
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Propanediol utilization protein pdua | protein | 90 | 34% helix, 38% strand | P0A1C7 |
| B | Propanediol utilization protein pdua | protein | 88 | 34% helix, 41% strand | P0A1C7 |
| C, D | Propanediol utilization protein pdua | protein | 88 | 39% helix, 39% strand | P0A1C7 |
| E, F | Propanediol utilization protein pdua | protein | 85 | 40% helix, 39% strand | P0A1C7 |
| G | Propanediol utilization protein pdua | protein | 87 | 37% helix, 39% strand | P0A1C7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, G, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.69 | 0.77 | 59 | SO4 |
| 2 | 110 | 0.54 | 0.83 | 23 | empty |
| 3 | 94 | 0.53 | 0.84 | 21 | empty |
| 4 | 117 | 0.44 | 0.77 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 848 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 839 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 822 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 802 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 444 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4QIG · Crystal Structure of PduA with edge mutation K26A and pore mutation S40C · the same entry in another collection · chain G against G, TM-score 1.00
- P0A1C7 · AlphaFold monomer V2.0 prediction for propanediol utilization protein pdua (P0A1C7) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 4QIG · PDBe 4QIG · UniProt P0A1C7
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