Research workbench
Crystal structure of full-length split GFP mutant D21H/K26H with copper mediated crystal contacts, P 21 21 21 space group
Analyse Crystal structure of full-length split GFP mutant D21H/K26H with copper… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W7D
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein D21H/K26H
- Ligands
- CRO, CU, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein D21H/K26H | protein | 224 | 11% helix, 52% strand | — |
| B | Fluorescent protein D21H/K26H | protein | 223 | 9% 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 · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.79 | 0.99 | 27 | CRO |
| 2 | 106 | 0.78 | 0.98 | 28 | CRO |
| 3 | 673 | 0.66 | 0.75 | 76 | GOL |
| 4 | 60 | 0.38 | 0.80 | 17 | empty |
| 5 | 110 | 0.37 | 0.74 | 19 | NHE |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 4W7D · Crystal Structure of Full-Length Split GFP Mutant D21H/K26H With Copper Mediated Crystal… · 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 4W7D · PDBe 4W7D
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