Research workbench
Structure of the yellow-green fluorescent protein mneongreen from branchiostoma lanceolatum at the acidic pH 4.5
Analyse Structure of the yellow-green fluorescent protein mneongreen from branchiostoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LTP
- Type
- protein
- Length
- 1,332 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mneongreen
- Ligands
- CR2, CL
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mneongreen | protein | 218 | 8% helix, 57% strand | — |
| B | Mneongreen | protein | 225 | 8% helix, 56% strand | — |
| C | Mneongreen | protein | 222 | 9% helix, 57% strand | — |
| D, F | Mneongreen | protein | 223 | 8% helix, 56% strand | — |
| E | Mneongreen | protein | 221 | 9% helix, 57% strand | — |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- FLC · Citrate anion · additive · 3 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.75 | 0.85 | 57 | empty |
| 2 | 817 | 0.73 | 0.79 | 62 | empty |
| 3 | 66 | 0.73 | 0.98 | 25 | CR2, CL |
| 4 | 500 | 0.73 | 0.82 | 57 | empty |
| 5 | 68 | 0.73 | 0.98 | 25 | CR2, CL |
Interfaces
12 interfaces between chains.
- D–F · 771 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 727 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 680 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 599 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor (chromophore).
Compared structures
- 5LTP · Structure of the Yellow-Green Fluorescent Protein mNeonGreen from Branchiostoma… · 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 5LTP · PDBe 5LTP
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