MolNFT v1 · #120685 · protein
Crystal structure of mrojoa mutant - P63H - W143S
5H87 · Mrojoa fluorescent protein: “Crystal structure of mrojoa mutant - P63H - W143S”. X-ray diffraction, 1 ligand (CH6), 15 pockets (best druggability 0.76). MolNFT v1 #120685 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H87
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mrojoa fluorescent protein
- Ligands
- CH6
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mrojoa fluorescent protein | protein | 213 | 4% 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.76 | 0.97 | 30 | CH6 |
| 2 | 92 | 0.76 | 0.97 | 28 | CH6 |
| 3 | 92 | 0.76 | 0.97 | 30 | CH6 |
| 4 | 80 | 0.75 | 0.98 | 28 | CH6 |
| 5 | 131 | 0.57 | 0.83 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1083 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 634 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 5H87 · Crystal structure of mRojoA mutant - P63H - W143S · 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 5H87 · PDBe 5H87
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