Research workbench
Crystal structure of full-length split GFP mutant D102C disulfide dimer, P 21 21 21 space group
Analyse Crystal structure of full-length split GFP mutant D102C disulfide dimer, P 21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W6P
- Type
- protein
- Length
- 1,612 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein D102C
- Ligands
- CRO
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein D102C | protein | 217 | 7% helix, 54% strand | — |
| B | Fluorescent protein D102C | protein | 214 | 8% helix, 53% strand | — |
| C | Fluorescent protein D102C | protein | 198 | 8% helix, 56% strand | — |
| D | Fluorescent protein D102C | protein | 202 | 4% helix, 55% strand | — |
| E | Fluorescent protein D102C | protein | 209 | 11% helix, 54% strand | — |
| F | Fluorescent protein D102C | protein | 214 | 7% helix, 55% strand | — |
| G | Fluorescent protein D102C | protein | 198 | 8% helix, 54% strand | — |
| H | Fluorescent protein D102C | protein | 160 | 5% helix, 51% 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 · 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
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.81 | 0.97 | 28 | CRO |
| 2 | 150 | 0.80 | 0.96 | 30 | CRO |
| 3 | 148 | 0.80 | 0.96 | 28 | CRO |
| 4 | 125 | 0.79 | 0.97 | 29 | CRO |
| 5 | 800 | 0.78 | 0.82 | 75 | empty |
Interfaces
11 interfaces between chains.
- D–H · 957 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 792 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 456 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 430 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 4 disulfide (chromophore, disulfide).
Compared structures
- 4W6P · Crystal Structure of Full-Length Split GFP Mutant D102C Disulfide Dimer, P 21 21 21 Space… · 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 4W6P · PDBe 4W6P
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