MolNFT v1 · #120687 · protein
Crystal structure of mrojoa mutant - T16V - P63Y - W143G - L163V
5H89 · Mrojoa fluorescent protein: “Crystal structure of mrojoa mutant - T16V - P63Y - W143G - L163V”. X-ray diffraction, 1 ligand (CH6), 13 pockets (best druggability 0.72). MolNFT v1 #120687 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5H89
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mrojoa fluorescent protein
- Ligands
- CH6
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mrojoa fluorescent protein | protein | 215 | 4% helix, 58% 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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.72 | 0.96 | 28 | CH6 |
| 2 | 62 | 0.71 | 0.97 | 26 | CH6 |
| 3 | 52 | 0.68 | 0.97 | 19 | CH6 |
| 4 | 334 | 0.68 | 0.82 | 51 | CH6 |
| 5 | 174 | 0.60 | 0.83 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–C · 988 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 654 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 272 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 255 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 5H89 · Crystal structure of mRojoA mutant - T16V - P63Y - W143G - 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 5H89 · PDBe 5H89
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