MolNFT v2 · #24834 · protein
Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab
1V7M · Monoclonal TN1 Fab Light Chain: “Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab”. X-ray diffraction at 2.51, 12 pockets (best druggability 0.69). MolNFT v2 #24834 on GenesisL1: 3D structure…
- PDB
- 1V7M
- Type
- protein
- Length
- 1,148 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.51
- Source
- Homo sapiens; Mus musculus
- Molecule
- Monoclonal TN1 Fab Light Chain; Monoclonal TN1 Fab Heavy Chain; Thrombopoietin
- UniProt
- P40225
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.51 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Monoclonal TN1 Fab Light Chain | protein | 212 | 6% helix, 54% strand | — |
| H, I | Monoclonal TN1 Fab Heavy Chain | protein | 217 | 7% helix, 52% strand | — |
| V, X | Thrombopoietin | protein | 145 | 56% helix, 6% strand | P40225 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.69 | 0.77 | 52 | empty |
| 2 | 356 | 0.60 | 0.77 | 46 | empty |
| 3 | 528 | 0.60 | 0.74 | 56 | empty |
| 4 | 114 | 0.59 | 0.86 | 29 | empty |
| 5 | 465 | 0.59 | 0.74 | 52 | empty |
Interfaces
8 interfaces between chains.
- M–I · 1704 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 1626 Ų buried · 14 hydrogen bonds · protein-protein
- I–X · 515 Ų buried · 8 hydrogen bonds · protein-protein
- H–V · 515 Ų buried · 9 hydrogen bonds · protein-protein
- M–X · 383 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1V7M · Human thrombopoietin functional domain complexed to neutralizing antibody TN1 Fab · the same entry in another collection · chain L against L, TM-score 1.00
- P40225 · AlphaFold monomer V2.0 prediction for thrombopoietin (P40225) · a predicted model of the same protein · chain V against A, TM-score 0.94
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 P40225
- Elsewhere: RCSB PDB 1V7M · PDBe 1V7M · UniProt P40225
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