Research workbench
Structure of the yellow fluorescent protein lanyfp from branchiostoma lanceolatum at pH 7.5
Analyse Structure of the yellow fluorescent protein lanyfp from branchiostoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LTQ
- Type
- protein
- Length
- 3,444 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein blfp-Y3
- UniProt
- B1PNC0
- Ligands
- CR2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein blfp-Y3 | protein | 217 | 8% helix, 55% strand | B1PNC0 |
| D | Green fluorescent protein blfp-Y3 | protein | 218 | 9% helix, 56% strand | B1PNC0 |
| B, C, P | Green fluorescent protein blfp-Y3 | protein | 216 | 9% helix, 57% strand | B1PNC0 |
| E, H, I, K | Green fluorescent protein blfp-Y3 | protein | 214 | 9% helix, 57% strand | B1PNC0 |
| F | Green fluorescent protein blfp-Y3 | protein | 221 | 10% helix, 55% strand | B1PNC0 |
| G, L | Green fluorescent protein blfp-Y3 | protein | 215 | 8% helix, 57% strand | B1PNC0 |
| J | Green fluorescent protein blfp-Y3 | protein | 221 | 10% helix, 55% strand | B1PNC0 |
| M | Green fluorescent protein blfp-Y3 | protein | 207 | 8% helix, 58% strand | B1PNC0 |
| N | Green fluorescent protein blfp-Y3 | protein | 216 | 9% helix, 54% strand | B1PNC0 |
| O | Green fluorescent protein blfp-Y3 | protein | 210 | 8% helix, 53% strand | B1PNC0 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 16 copies · chains A, D, B, C, E, H, F, G, I, L, J, K, M, P, N, O
- CL · Chloride ion · ion · 16 copies · chains A, D, B, C, E, H, F, G, I, L, J, K, M, P, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.87 | 0.88 | 113 | empty |
| 2 | 1122 | 0.87 | 0.88 | 123 | empty |
| 3 | 1164 | 0.86 | 0.87 | 145 | empty |
| 4 | 983 | 0.85 | 0.87 | 123 | empty |
| 5 | 617 | 0.84 | 0.89 | 75 | empty |
Interfaces
40 interfaces between chains.
- H–F · 1243 Ų buried · 14 hydrogen bonds · protein-protein
- L–J · 1201 Ų buried · 13 hydrogen bonds · protein-protein
- I–K · 1098 Ų buried · 9 hydrogen bonds · protein-protein
- P–N · 1086 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 1086 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (chromophore).
Compared structures
- 5LTQ · Structure of the Yellow Fluorescent Protein lanYFP from Branchiostoma lanceolatum at pH… · the same entry in another collection · chain G against G, 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
- Every structure of UniProt B1PNC0
- Elsewhere: RCSB PDB 5LTQ · PDBe 5LTQ · UniProt B1PNC0
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