MolNFT v1 · #118598 · protein
Sandercyanin fluorescent protein purified from sander vitreus
5F6Z: “Sandercyanin fluorescent protein purified from sander vitreus”. X-ray diffraction, 2 ligands (BLA, NAG), 9 pockets (best druggability 0.79). MolNFT v1 #118598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F6Z
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sandercyanin fluorescent protein
- Ligands
- BLA, NAG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sandercyanin fluorescent protein | protein | 166 | 14% helix, 45% strand | — |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 4 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.79 | 0.89 | 43 | BLA |
| 2 | 335 | 0.78 | 0.88 | 43 | BLA |
| 3 | 325 | 0.78 | 0.89 | 43 | BLA |
| 4 | 371 | 0.78 | 0.87 | 42 | BLA |
| 5 | 953 | 0.72 | 0.76 | 95 | empty |
Interfaces
6 interfaces between chains.
- B–C · 678 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 671 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 665 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 250 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5F6Z · Sandercyanin Fluorescent Protein purified from Sander vitreus · the same entry in another collection · chain B against B, 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 5F6Z · PDBe 5F6Z
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