MolNFT v1 · #186415 · protein
Crystal structure of TSPAN15 large extracellular loop (TSPAN15 lel) in complex with 1C12 Fab
7RD5 · 1C12 Fab light chain: “Crystal structure of TSPAN15 large extracellular loop (TSPAN15 lel) in complex with 1C12 Fab”. X-ray diffraction, 11 pockets (best druggability 0.67). MolNFT v1 #186415 on GenesisL1: 3D structure, binding…
- 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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