MolNFT v1 · #126373 · protein
Synthetic nanobody in complex with mbp
5M14 · Maltose-binding periplasmic protein: “Synthetic nanobody in complex with mbp”. X-ray diffraction, 9 pockets (best druggability 0.82). MolNFT v1 #126373 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M14
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; Synthetic nanobody L2_G11 (a-MBP#2)
- UniProt
- P0AEX9
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltose-binding periplasmic protein | protein | 366 | 45% helix, 19% strand | P0AEX9 |
| C, D | Synthetic nanobody L2_G11 (a-MBP#2) | protein | 127 | 5% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.82 | 0.85 | 77 | empty |
| 2 | 365 | 0.62 | 0.78 | 42 | empty |
| 3 | 339 | 0.61 | 0.78 | 46 | empty |
| 4 | 258 | 0.61 | 0.80 | 44 | empty |
| 5 | 275 | 0.58 | 0.78 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1172 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 227 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M14 · 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 5M14 · PDBe 5M14 · UniProt P0AEX9
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