MolNFT v1 · #126374 · protein
Synthetic nanobody in complex with mbp
5M15 · Maltose-binding periplasmic protein: “Synthetic nanobody in complex with mbp”. X-ray diffraction, 9 pockets (best druggability 0.79). MolNFT v1 #126374 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M15
- Type
- protein
- Length
- 985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; Synthetic nanobody L2_D09, (a-MBP#3)
- UniProt
- P0AEX9
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein | protein | 366 | 45% helix, 19% strand | P0AEX9 |
| B | Maltose-binding periplasmic protein | protein | 367 | 45% helix, 21% strand | P0AEX9 |
| C | Synthetic nanobody L2_D09, (a-MBP#3) | protein | 127 | 2% helix, 50% strand | — |
| D | Synthetic nanobody L2_D09, (a-MBP#3) | protein | 125 | 10% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.79 | 0.84 | 77 | empty |
| 2 | 779 | 0.71 | 0.77 | 94 | empty |
| 3 | 273 | 0.68 | 0.83 | 30 | empty |
| 4 | 243 | 0.55 | 0.77 | 41 | empty |
| 5 | 89 | 0.53 | 0.84 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1194 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 606 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 187 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M15 · Synthetic nanobody in complex with MBP · 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 5M15 · PDBe 5M15 · UniProt P0AEX9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.