MolNFT v1 · #108430 · protein
Crystal structure of full-length split GFP mutant D117C disulfide dimer, P 63 space group
4W6M · Fluorescent protein D117C: “Crystal structure of full-length split GFP mutant D117C disulfide dimer, P 63 space group”. X-ray diffraction, 1 ligand (CRO), 13 pockets (best druggability 0.79). MolNFT v1 #108430 on GenesisL1: 3D…
- PDB
- 4W6M
- Type
- protein
- Length
- 838 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein D117C
- Ligands
- CRO
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fluorescent protein D117C | protein | 221 | 10% helix, 53% strand | — |
| C | Fluorescent protein D117C | protein | 214 | 7% helix, 53% strand | — |
| D | Fluorescent protein D117C | protein | 182 | 5% helix, 53% 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
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.79 | 0.98 | 30 | CRO |
| 2 | 119 | 0.79 | 0.98 | 27 | CRO |
| 3 | 116 | 0.78 | 0.97 | 30 | CRO |
| 4 | 360 | 0.73 | 0.84 | 48 | CRO |
| 5 | 537 | 0.65 | 0.76 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–B · 841 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 773 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 disulfide (chromophore, disulfide).
Compared structures
- 4W6M · Crystal Structure of Full-Length Split GFP Mutant D117C Disulfide Dimer, P 63 Space Group · 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 4W6M · PDBe 4W6M
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