Research workbench
Crystal structure of a thermostable green fluorescent protein (tgp) with a synthetic nanobody (SB44)
Analyse Crystal structure of a thermostable green fluorescent protein (tgp) with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LZ2
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable green fluorescent protein; Synthetic nanobody (sybody) 44 against the…
- Ligands
- CRQ, NA
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable green fluorescent protein | protein | 215 | 5% helix, 58% strand | — |
| B | Synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (tgp) | protein | 117 | 3% helix, 49% strand | — |
| C | Thermostable green fluorescent protein | protein | 217 | 5% helix, 57% strand | — |
| D | Synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (tgp) | protein | 119 | 3% helix, 50% strand | — |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains B, C, D
- GOL · Glycerol · additive · 2 copies · chains C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.75 | 0.98 | 26 | CRQ |
| 2 | 79 | 0.75 | 0.98 | 26 | CRQ |
| 3 | 164 | 0.59 | 0.83 | 34 | empty |
| 4 | 148 | 0.54 | 0.80 | 23 | NA |
| 5 | 129 | 0.44 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 890 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 889 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 738 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (chromophore, disulfide).
Compared structures
- 6LZ2 · Crystal structure of a thermostable green fluorescent protein (TGP) with a synthetic… · 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 6LZ2 · PDBe 6LZ2
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