Research workbench
Human thrombopoietin functional domain complexed to neutralizing antibody TN1 Fab
Analyse Human thrombopoietin functional domain complexed to neutralizing antibody TN1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V7N
- Type
- protein
- Length
- 2,278 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal TN1 Fab light chain; Monoclonal TN1 Fab heavy chain; Thrombopoietin
- UniProt
- P40225
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, O | Monoclonal TN1 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| H, I, J, K | Monoclonal TN1 Fab heavy chain | protein | 217 | 7% helix, 46% strand | — |
| M, N | Monoclonal TN1 Fab light chain | protein | 212 | 6% helix, 47% strand | — |
| V | Thrombopoietin | protein | 145 | 61% helix, 6% strand | P40225 |
| X | Thrombopoietin | protein | 138 | 61% helix, 6% strand | P40225 |
| Y | Thrombopoietin | protein | 139 | 63% helix, 4% strand | P40225 |
| Z | Thrombopoietin | protein | 138 | 64% helix, 6% strand | P40225 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.82 | 0.88 | 83 | empty |
| 2 | 1026 | 0.82 | 0.83 | 118 | empty |
| 3 | 1198 | 0.80 | 0.81 | 131 | empty |
| 4 | 625 | 0.77 | 0.83 | 66 | empty |
| 5 | 465 | 0.76 | 0.84 | 65 | empty |
Interfaces
29 interfaces between chains.
- L–H · 1656 Ų buried · 18 hydrogen bonds · protein-protein
- N–J · 1648 Ų buried · 15 hydrogen bonds · protein-protein
- O–K · 1648 Ų buried · 17 hydrogen bonds · protein-protein
- M–I · 1631 Ų buried · 15 hydrogen bonds · protein-protein
- Y–Z · 741 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 1V7N · Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab · the same entry in another collection · chain Z against Z, 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 P40225
- Elsewhere: RCSB PDB 1V7N · PDBe 1V7N · UniProt P40225
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