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Crystal structure of maltose binding protein in complex with an allosteric synthetic antibody
Analyse Crystal structure of maltose binding protein in complex with an allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BJZ
- Type
- protein
- Length
- 1,617 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; Synthetic antibody, Fab fragment, heavy chain…
- UniProt
- P0AEY0
- Ligands
- GLC, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Maltose-binding periplasmic protein | protein | 365 | 45% helix, 21% strand | P0AEY0 |
| C | Synthetic antibody, Fab fragment, heavy chain | protein | 228 | 7% helix, 49% strand | — |
| L, H | Synthetic antibody, Fab fragment, light chain | protein | 213 | 6% helix, 52% strand | — |
| A | Maltose-binding periplasmic protein | protein | 367 | 46% helix, 21% strand | P0AEY0 |
| D | Synthetic antibody, Fab fragment, heavy chain | protein | 231 | 9% helix, 48% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains L, A, H
- GOL · Glycerol · additive · 5 copies · chains B, A, D, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.73 | 0.98 | 27 | empty |
| 2 | 67 | 0.72 | 0.97 | 24 | empty |
| 3 | 322 | 0.71 | 0.84 | 33 | GLC |
| 4 | 326 | 0.71 | 0.84 | 36 | GLC |
| 5 | 433 | 0.70 | 0.81 | 53 | empty |
Interfaces
10 interfaces between chains.
- D–H · 1878 Ų buried · 12 hydrogen bonds · protein-protein
- C–L · 1832 Ų buried · 8 hydrogen bonds · protein-protein
- C–A · 744 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 743 Ų buried · 5 hydrogen bonds · protein-protein
- B–H · 694 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5BJZ · Crystal structure of maltose binding protein in complex with an allosteric synthetic… · the same entry in another collection · chain B against B, 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 P0AEY0
- Elsewhere: RCSB PDB 5BJZ · PDBe 5BJZ · UniProt P0AEY0
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