MolNFT v1 · #114224 · protein
Extra-superfolder GFP
5B61 · Green fluorescent protein: “Extra-superfolder GFP”. X-ray diffraction, 16 pockets (best druggability 0.72). MolNFT v1 #114224 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B61
- Type
- protein
- Length
- 1,349 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 222 | 10% helix, 53% strand | — |
| B | Green fluorescent protein | protein | 224 | 12% helix, 52% strand | — |
| C | Green fluorescent protein | protein | 226 | 12% helix, 52% strand | — |
| D, E | Green fluorescent protein | protein | 227 | 10% helix, 51% strand | — |
| F | Green fluorescent protein | protein | 223 | 12% helix, 52% strand | — |
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.72 | 0.98 | 21 | empty |
| 2 | 436 | 0.61 | 0.76 | 62 | empty |
| 3 | 333 | 0.58 | 0.77 | 42 | empty |
| 4 | 376 | 0.58 | 0.76 | 53 | empty |
| 5 | 332 | 0.58 | 0.76 | 52 | empty |
Interfaces
5 interfaces between chains.
- B–E · 688 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 678 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 677 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 347 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 343 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5B61 · Extra-superfolder GFP · 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 5B61 · PDBe 5B61
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