MolNFT v1 · #103434 · protein
Crystal structure of a trap periplasmic solute binding protein from desulfovibrio alaskensis G20 (DDE_0634, target efi-510120) with bound indole pyruvate
4PGN · Extracellular solute-binding protein, family 7: “Crystal structure of a trap periplasmic solute binding protein from desulfovibrio alaskensis G20 (DDE_0634…”. X-ray diffraction, 1 ligand (3IO), 19 pockets (best druggability 0.82).…
- PDB
- 4PGN
- Type
- protein
- Length
- 1,237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein, family 7
- UniProt
- Q315G1
- Ligands
- 3IO
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein, family 7 | protein | 308 | 51% helix, 19% strand | Q315G1 |
| B | Extracellular solute-binding protein, family 7 | protein | 309 | 52% helix, 18% strand | Q315G1 |
| C, D | Extracellular solute-binding protein, family 7 | protein | 310 | 52% helix, 18% strand | Q315G1 |
Ligands and binding sites
- 3IO · 3-(1H-indol-3-yl)-2-oxopropanoic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.82 | 0.83 | 114 | empty |
| 2 | 58 | 0.74 | 0.99 | 17 | 3IO |
| 3 | 58 | 0.73 | 0.98 | 17 | 3IO |
| 4 | 56 | 0.72 | 0.98 | 17 | 3IO |
| 5 | 220 | 0.64 | 0.83 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–D · 735 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 584 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 196 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 94 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4PGN · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO… · the same entry in another collection · chain D against D, TM-score 1.00
- Q315G1 · AlphaFold monomer V2.0 prediction for solute-binding protein DDE_0634 (Q315G1) · a predicted model of the same protein · chain D 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 Q315G1
- Elsewhere: RCSB PDB 4PGN · PDBe 4PGN · UniProt Q315G1
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