MolNFT v1 · #108469 · protein
Crystal structure of full-length split GFP mutant E124H/K126H copper mediated dimer, P 21 space group
4W7R · Fluorescent protein E124H/K126C: “Crystal structure of full-length split GFP mutant E124H/K126H copper mediated dimer, P 21 space group”. X-ray diffraction, 2 ligands (CRO, CU), 10 pockets (best druggability 0.79). MolNFT v1 #108469…
- PDB
- 4W7R
- Type
- protein
- Length
- 899 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein E124H/K126C
- Ligands
- CRO, CU
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein E124H/K126C | protein | 225 | 10% helix, 52% strand | — |
| B | Fluorescent protein E124H/K126C | protein | 224 | 11% helix, 52% strand | — |
| C, D | Fluorescent protein E124H/K126C | protein | 225 | 11% helix, 52% strand | — |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.79 | 0.99 | 28 | CRO |
| 2 | 110 | 0.79 | 0.98 | 26 | CRO |
| 3 | 104 | 0.78 | 0.97 | 27 | CRO |
| 4 | 88 | 0.77 | 0.98 | 25 | CRO |
| 5 | 849 | 0.71 | 0.76 | 68 | EDO |
Interfaces
4 interfaces between chains.
- B–C · 359 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 265 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 211 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 206 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4W7R · Crystal Structure of Full-Length Split GFP Mutant E124H/K126H Copper Mediated Dimer, P 21… · 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 4W7R · PDBe 4W7R
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