MolNFT v1 · #111155 · protein
Crystal structure of a trap transporter solute binding protein (IPR025997) from bordetella bronchiseptica RB50 (BB0280, target efi- 500035) with bound picolinic acid
4YIC: “Crystal structure of a trap transporter solute binding protein (IPR025997) from bordetella bronchiseptica…”. X-ray diffraction, 2 ligands (6PC, CA), 10 pockets (best druggability 0.75). MolNFT v1 #111155 on GenesisL1: 3D structure…
- PDB
- 4YIC
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap transporter solute binding protein
- UniProt
- X5ID49
- Ligands
- 6PC, CA
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap transporter solute binding protein | protein | 344 | 56% helix, 15% strand | X5ID49 |
| B | Trap transporter solute binding protein | protein | 343 | 55% helix, 15% strand | X5ID49 |
Ligands and binding sites
- 6PC · Pyridine-2-carboxylic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.98 | 17 | empty |
| 2 | 58 | 0.72 | 0.98 | 15 | empty |
| 3 | 67 | 0.72 | 0.97 | 23 | 6PC |
| 4 | 70 | 0.72 | 0.97 | 23 | CA, 6PC |
| 5 | 105 | 0.47 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3500 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4YIC · Crystal structure of a trap transporter solute binding protein (IPR025997) from… · 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 X5ID49
- Elsewhere: RCSB PDB 4YIC · PDBe 4YIC · UniProt X5ID49
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