MolNFT v1 · #96173 · protein
Isolation, cloning and biophysical analysis of a novel hexameric green fluorescent protein from a philippine soft coral
4JC2 · ASFP504: “Isolation, cloning and biophysical analysis of a novel hexameric green fluorescent protein from a philippine…”. X-ray diffraction, 1 ligand (CRQ), 12 pockets (best druggability 0.76). MolNFT v1 #96173 on GenesisL1: 3D…
- PDB
- 4JC2
- Type
- protein
- Length
- 1,319 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASFP504
- Ligands
- CRQ
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | ASFP504 | protein | 220 | 3% helix, 56% strand | — |
| C | ASFP504 | protein | 219 | 4% helix, 57% strand | — |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.76 | 0.98 | 29 | CRQ |
| 2 | 80 | 0.75 | 0.98 | 27 | CRQ |
| 3 | 77 | 0.75 | 0.98 | 24 | CRQ |
| 4 | 77 | 0.73 | 0.97 | 27 | CRQ |
| 5 | 74 | 0.72 | 0.97 | 25 | CRQ |
Interfaces
7 interfaces between chains.
- D–F · 1614 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1605 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 1588 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 293 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor (chromophore).
Compared structures
- 4JC2 · Isolation, Cloning and Biophysical Analysis of a Novel Hexameric Green Fluorescent… · the same entry in another collection · chain F against F, 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 4JC2 · PDBe 4JC2
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