Research workbench
MSANDY2
Analyse MSANDY2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RY2
- Type
- protein
- Length
- 1,715 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MSANDY2
- Ligands
- CH6, NRQ
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | MSANDY2 | protein | 215 | 4% helix, 58% strand | — |
| B, D, G | MSANDY2 | protein | 214 | 4% helix, 58% strand | — |
| H | MSANDY2 | protein | 213 | 5% 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 · 6 copies · chains A, B, C, D, F, G
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains E, H
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 | 720 | 0.79 | 0.83 | 83 | empty |
| 2 | 71 | 0.74 | 0.98 | 18 | CH6 |
| 3 | 72 | 0.73 | 0.97 | 20 | CH6 |
| 4 | 65 | 0.72 | 0.97 | 21 | CH6 |
| 5 | 72 | 0.72 | 0.96 | 20 | NRQ |
Interfaces
10 interfaces between chains.
- C–D · 621 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 615 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 363 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 343 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 331 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 7RY2 · mSandy2 · 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 7RY2 · PDBe 7RY2
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