MolNFT v1 · #102990 · protein
Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the pdu microcompartment
4P2S · Putative propanediol utilization protein pdua: “Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.48).…
- PDB
- 4P2S
- Type
- protein
- Length
- 792 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative propanediol utilization protein pdua
- UniProt
- V1FW89
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Putative propanediol utilization protein pdua | protein | 88 | 35% helix, 39% strand | V1FW89 |
| B | Putative propanediol utilization protein pdua | protein | 89 | 38% helix, 37% strand | V1FW89 |
| C, E, G | Putative propanediol utilization protein pdua | protein | 87 | 41% helix, 38% strand | V1FW89 |
| D | Putative propanediol utilization protein pdua | protein | 88 | 35% helix, 39% strand | V1FW89 |
| F | Putative propanediol utilization protein pdua | protein | 89 | 38% helix, 38% strand | V1FW89 |
| H | Putative propanediol utilization protein pdua | protein | 89 | 35% helix, 38% strand | V1FW89 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, H, D, C, I
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F, G, H, I
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.48 | 0.79 | 25 | GOL |
| 2 | 241 | 0.46 | 0.73 | 26 | GOL, SO4 |
| 3 | 93 | 0.35 | 0.74 | 21 | empty |
| 4 | 64 | 0.35 | 0.77 | 18 | SO4 |
Interfaces
10 interfaces between chains.
- C–D · 907 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 895 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 866 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 865 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 862 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4P2S · Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to… · 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 V1FW89
- Elsewhere: RCSB PDB 4P2S · PDBe 4P2S · UniProt V1FW89
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