Research workbench
Crystal structure of a trap periplasmic solute binding protein from haemophilus influenzae rdaw (HICG_00826, target efi-510123) with bound L-gulonate
Analyse Crystal structure of a trap periplasmic solute binding protein from haemophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PBQ
- Type
- protein
- Length
- 912 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative trap periplasmic solute binding protein
- UniProt
- C9MHP2
- Ligands
- 2UF, SO4
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative trap periplasmic solute binding protein | protein | 304 | 53% helix, 20% strand | C9MHP2 |
Ligands and binding sites
- 2UF · L-gulonate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.86 | 0.91 | 99 | 2UF, PEG |
| 2 | 76 | 0.66 | 0.93 | 26 | 2UF |
| 3 | 85 | 0.65 | 0.91 | 24 | empty |
| 4 | 90 | 0.65 | 0.90 | 22 | MES |
| 5 | 64 | 0.61 | 0.91 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 778 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4PBQ · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM HAEMOPHILUS… · 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 C9MHP2
- Elsewhere: RCSB PDB 4PBQ · PDBe 4PBQ · UniProt C9MHP2
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