MolNFT v1 · #114318 · protein
Crystal structure of maltose binding protein in complex with an endosteric synthetic antibody
5BK1 · Synthetic antibody, Fab fragment, heavy chain: “Crystal structure of maltose binding protein in complex with an endosteric synthetic antibody”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.79). MolNFT v1 #114318…
- PDB
- 5BK1
- Type
- protein
- Length
- 1,604 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synthetic antibody, Fab fragment, heavy chain; Synthetic antibody, Fab fragment, light…
- Ligands
- CL
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Synthetic antibody, Fab fragment, heavy chain | protein | 227 | 8% helix, 51% strand | — |
| L | Synthetic antibody, Fab fragment, light chain | protein | 210 | 8% helix, 49% strand | — |
| C | Synthetic antibody, Fab fragment, heavy chain | protein | 226 | 9% helix, 50% strand | — |
| D | Synthetic antibody, Fab fragment, light chain | protein | 209 | 6% helix, 49% strand | — |
| A, B | Maltose binding protein | protein | 366 | 45% helix, 20% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.79 | 0.80 | 143 | CL |
| 2 | 844 | 0.76 | 0.80 | 98 | empty |
| 3 | 60 | 0.70 | 0.97 | 22 | empty |
| 4 | 264 | 0.61 | 0.80 | 37 | empty |
| 5 | 451 | 0.60 | 0.75 | 54 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2021 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1899 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 978 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 977 Ų buried · 16 hydrogen bonds · protein-protein
- H–C · 614 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5BK1 · Crystal structure of maltose binding protein in complex with an endosteric synthetic… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 5BK1 · PDBe 5BK1
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