Research workbench
Crystal structure of LSSMKATE2 red fluorescent proteins with large stokes shift
Analyse Crystal structure of LSSMKATE2 red fluorescent proteins with large stokes shift in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NT3
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LSSMKATE2 red fluorescent protein
- Ligands
- NRQ
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | LSSMKATE2 red fluorescent protein | protein | 223 | 5% helix, 56% strand | — |
| C | LSSMKATE2 red fluorescent protein | protein | 224 | 6% helix, 55% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.83 | 0.85 | 113 | empty |
| 2 | 134 | 0.79 | 0.97 | 34 | NRQ |
| 3 | 130 | 0.78 | 0.97 | 35 | NRQ |
| 4 | 136 | 0.77 | 0.95 | 32 | NRQ |
| 5 | 123 | 0.77 | 0.96 | 32 | NRQ |
Interfaces
6 interfaces between chains.
- C–D · 1466 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1458 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 997 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 992 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 3NT3 · CRYSTAL STRUCTURE OF LSSmKate2 red fluorescent proteins with large Stokes shift · 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 3NT3 · PDBe 3NT3
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