MolNFT v1 · #187463 · protein
Branchiostoma floridae fluorescent protein LANFP10A2
7SFA: “Branchiostoma floridae fluorescent protein LANFP10A2”. X-ray diffraction, 1 ligand (JBY), 14 pockets (best druggability 0.87). MolNFT v1 #187463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SFA
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein LANFP10A2
- Ligands
- JBY
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein LANFP10A2 | protein | 215 | 10% helix, 57% strand | — |
| B | Fluorescent protein LANFP10A2 | protein | 221 | 10% helix, 56% strand | — |
| C | Fluorescent protein LANFP10A2 | protein | 216 | 10% helix, 57% strand | — |
| D | Fluorescent protein LANFP10A2 | protein | 217 | 10% helix, 56% strand | — |
Ligands and binding sites
- JBY · (2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl) methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic acid · ligand · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.87 | 0.88 | 110 | empty |
| 2 | 105 | 0.78 | 0.98 | 34 | JBY |
| 3 | 98 | 0.77 | 0.98 | 29 | JBY |
| 4 | 100 | 0.76 | 0.97 | 35 | JBY |
| 5 | 88 | 0.75 | 0.97 | 26 | JBY |
Interfaces
6 interfaces between chains.
- B–C · 1207 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1198 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1005 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 124 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7SFA · Branchiostoma floridae fluorescent protein LanFP10A2 · 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 7SFA · PDBe 7SFA
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