Research workbench
Fluorogen activating protein M8VLA4(S55P) in complex with dimethylindole red
Analyse Fluorogen activating protein M8VLA4(S55P) in complex with dimethylindole red in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T0X
- Type
- protein
- Length
- 220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin variable lambda domain M8VLA4(S55P)
- Ligands
- DIW, SO4
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin variable lambda domain M8VLA4(S55P) | protein | 111 | 3% helix, 50% strand | — |
| B | Immunoglobulin variable lambda domain M8VLA4(S55P) | protein | 109 | 7% helix, 45% strand | — |
Ligands and binding sites
- DIW · 1-(3-sulfopropyl)-4-[(1E,3E)-3-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)prop-1-en-1-yl]quinolinium · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.71 | 0.85 | 36 | DIW, SO4 |
Interfaces
1 interface between chains.
- A–B · 571 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 3T0X · Fluorogen Activating Protein M8VLA4(S55P) in complex with dimethylindole red · 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
- Elsewhere: RCSB PDB 3T0X · PDBe 3T0X
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