Research workbench
Crystal structure of a trap periplasmic solute binding protein from pseudomonas aeruginosa PAO1 (PA4616), target efi-510182, with bound L-malate
Analyse Crystal structure of a trap periplasmic solute binding protein from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NF0
- Type
- protein
- Length
- 2,213 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable C4-dicarboxylate-binding protein
- UniProt
- Q9HVH5
- Ligands
- LMR, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable C4-dicarboxylate-binding protein | protein | 291 | 47% helix, 20% strand | Q9HVH5 |
| B | Probable C4-dicarboxylate-binding protein | protein | 273 | 45% helix, 22% strand | Q9HVH5 |
| D | Probable C4-dicarboxylate-binding protein | protein | 289 | 48% helix, 22% strand | Q9HVH5 |
| E | Probable C4-dicarboxylate-binding protein | protein | 233 | 42% helix, 21% strand | Q9HVH5 |
| F | Probable C4-dicarboxylate-binding protein | protein | 288 | 48% helix, 23% strand | Q9HVH5 |
| G | Probable C4-dicarboxylate-binding protein | protein | 287 | 47% helix, 21% strand | Q9HVH5 |
| H | Probable C4-dicarboxylate-binding protein | protein | 261 | 46% helix, 21% strand | Q9HVH5 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 7 copies · chains A, B, C, D, F, G, H
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D, G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.77 | 0.81 | 83 | empty |
| 2 | 745 | 0.76 | 0.81 | 53 | empty |
| 3 | 683 | 0.75 | 0.81 | 71 | empty |
| 4 | 696 | 0.75 | 0.81 | 63 | empty |
| 5 | 990 | 0.75 | 0.78 | 76 | empty |
Interfaces
10 interfaces between chains.
- F–G · 756 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 709 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 643 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 579 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4NF0 · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOMONAS… · 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 Q9HVH5
- Elsewhere: RCSB PDB 4NF0 · PDBe 4NF0 · UniProt Q9HVH5
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