Research workbench
Complex of maltose-binding protein (mbp) with single-chain fv (scfv)
Analyse Complex of maltose-binding protein (mbp) with single-chain fv (scfv) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JTR
- Type
- protein
- Length
- 2,372 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic protein; Single-chain fv antibody fragment (scfv)
- UniProt
- P0AEX9
- Ligands
- GLC, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 369 | 45% helix, 21% strand | P0AEX9 |
| B | Single-chain fv antibody fragment (scfv) | protein | 225 | 7% helix, 51% strand | — |
| D | Single-chain fv antibody fragment (scfv) | protein | 223 | 7% helix, 51% strand | — |
| F, H | Single-chain fv antibody fragment (scfv) | protein | 224 | 7% helix, 52% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, C, E, G
- CL · Chloride ion · ion · 3 copies · chains B, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.72 | 0.84 | 31 | GLC |
| 2 | 278 | 0.71 | 0.85 | 30 | GLC |
| 3 | 316 | 0.70 | 0.83 | 29 | GLC |
| 4 | 275 | 0.70 | 0.84 | 31 | GLC |
| 5 | 218 | 0.56 | 0.79 | 38 | empty |
Interfaces
10 interfaces between chains.
- A–B · 772 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 736 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 735 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 717 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 579 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7JTR · Complex of maltose-binding protein (MBP) with single-chain Fv (scFv) · 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 P0AEX9
- Elsewhere: RCSB PDB 7JTR · PDBe 7JTR · UniProt P0AEX9
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