MolNFT v1 · #118283 · protein
Wild type green fluorescent protein dendfp (dendronephthya sp.)
5EXB: “Wild type green fluorescent protein dendfp (dendronephthya sp.)”. X-ray diffraction, 1 ligand (5SQ), 20 pockets (best druggability 0.86). MolNFT v1 #118283 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EXB
- Type
- protein
- Length
- 3,547 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q8T6U0
- Ligands
- 5SQ
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H, I, M, N | Green fluorescent protein | protein | 220 | 5% helix, 56% strand | Q8T6U0 |
| B, G | Green fluorescent protein | protein | 224 | 3% helix, 55% strand | Q8T6U0 |
| C | Green fluorescent protein | protein | 223 | 4% helix, 56% strand | Q8T6U0 |
| D | Green fluorescent protein | protein | 221 | 4% helix, 56% strand | Q8T6U0 |
| F, J, O, P | Green fluorescent protein | protein | 221 | 4% helix, 56% strand | Q8T6U0 |
| K | Green fluorescent protein | protein | 226 | 4% helix, 55% strand | Q8T6U0 |
| L | Green fluorescent protein | protein | 225 | 4% helix, 54% strand | Q8T6U0 |
Ligands and binding sites
- 5SQ · 2-[2-[(1S)-1-azanyl-2-(1H-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GOL · Glycerol · additive · 3 copies · chains B, C, E, I, N
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 | 1020 | 0.86 | 0.87 | 117 | empty |
| 2 | 1053 | 0.86 | 0.87 | 115 | empty |
| 3 | 918 | 0.85 | 0.87 | 132 | empty |
| 4 | 882 | 0.84 | 0.87 | 106 | empty |
| 5 | 731 | 0.80 | 0.84 | 68 | GOL |
Interfaces
37 interfaces between chains.
- K–N · 1781 Ų buried · 27 hydrogen bonds · protein-protein
- L–M · 1733 Ų buried · 29 hydrogen bonds · protein-protein
- G–I · 1703 Ų buried · 33 hydrogen bonds · protein-protein
- B–P · 1673 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 1650 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 covalent (covalent ligand).
Compared structures
- 5EXB · Wild type green fluorescent protein DendFP (Dendronephthya sp.) · the same entry in another collection · chain H against H, 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 Q8T6U0
- Elsewhere: RCSB PDB 5EXB · PDBe 5EXB · UniProt Q8T6U0
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