Research workbench
Crystal structure of mrojoa mutant - T16V -P63F - W143A - L163V
Analyse Crystal structure of mrojoa mutant - T16V -P63F - W143A - L163V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H88
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mrojoa fluorescent protein
- Ligands
- CH6
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mrojoa fluorescent protein | protein | 213 | 5% helix, 58% strand | — |
| B, C | Mrojoa fluorescent protein | protein | 212 | 4% helix, 58% strand | — |
| D | Mrojoa fluorescent protein | protein | 211 | 5% helix, 59% strand | — |
Ligands and binding sites
- CH6 · {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.77 | 0.97 | 31 | CH6 |
| 2 | 92 | 0.76 | 0.97 | 28 | CH6 |
| 3 | 62 | 0.72 | 0.98 | 23 | CH6 |
| 4 | 61 | 0.70 | 0.97 | 20 | CH6 |
| 5 | 171 | 0.61 | 0.83 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1002 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 5H88 · Crystal structure of mRojoA mutant - T16V -P63F - W143A - L163V · 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 5H88 · PDBe 5H88
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