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Crystal structure of full-length split GFP mutant E115C/T118H with metal mediated crystal contacts, P 1 21 1 space group
Analyse Crystal structure of full-length split GFP mutant E115C/T118H with metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W74
- Type
- protein
- Length
- 1,785 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein E115C/T118H
- Ligands
- CRO, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, H | Fluorescent protein E115C/T118H | protein | 223 | 11% helix, 52% strand | — |
| C | Fluorescent protein E115C/T118H | protein | 224 | 11% helix, 52% strand | — |
| D | Fluorescent protein E115C/T118H | protein | 221 | 10% helix, 52% strand | — |
| F, G | Fluorescent protein E115C/T118H | protein | 224 | 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 · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 6 copies · chains A, G, B, H, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.78 | 0.98 | 28 | CRO |
| 2 | 113 | 0.78 | 0.97 | 29 | CRO |
| 3 | 113 | 0.78 | 0.97 | 27 | CRO |
| 4 | 107 | 0.78 | 0.98 | 27 | CRO |
| 5 | 101 | 0.78 | 0.97 | 25 | CRO |
Interfaces
10 interfaces between chains.
- A–C · 905 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 902 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 538 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 513 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 508 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 4W74 · Crystal Structure of Full-Length Split GFP Mutant E115C/T118H With Metal 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 4W74 · PDBe 4W74
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