Research workbench
Crystal structure of TSPAN15 large extracellular loop (TSPAN15 lel) in complex with 1C12 Fab
Analyse Crystal structure of TSPAN15 large extracellular loop (TSPAN15 lel) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RD5
- Type
- protein
- Length
- 1,136 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1C12 Fab light chain; 1C12 Fab heavy chain; Tetraspanin-15
- UniProt
- O95858
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 1C12 Fab light chain | protein | 220 | 8% helix, 48% strand | — |
| B, D | 1C12 Fab heavy chain | protein | 226 | 8% helix, 47% strand | — |
| F, E | Tetraspanin-15 | protein | 122 | 48% helix, 3% strand | O95858 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.67 | 0.79 | 45 | empty |
| 2 | 365 | 0.64 | 0.79 | 47 | empty |
| 3 | 557 | 0.61 | 0.74 | 54 | empty |
| 4 | 452 | 0.57 | 0.73 | 51 | empty |
| 5 | 166 | 0.46 | 0.76 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2013 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1993 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 551 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 543 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 220 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 7RD5 · Crystal structure of Tspan15 large extracellular loop (Tspan15 LEL) in complex with 1C12… · the same entry in another collection · chain F against F, TM-score 1.00
- O95858 · AlphaFold monomer V2.0 prediction for tetraspanin-15 (O95858) · a predicted model of the same protein · chain F against A, TM-score 0.91
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 O95858
- Elsewhere: RCSB PDB 7RD5 · PDBe 7RD5 · UniProt O95858
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