Research workbench
Crystal structure of tsushimycin
Analyse Crystal structure of tsushimycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W3M
- Type
- protein
- Length
- 132 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tsushimycin
- Ligands
- LNG, CA, CL
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Tsushimycin | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- LNG · Delta-3isotetradecenoic acid · ligand · 12 copies · chains A, B, G, C, D, E, F, H, I, J, K, L
- CA · Calcium ion · metal · 25 copies · chains A, B, G, C, E, D, L, F, J, H, I, K
- CL · Chloride ion · ion · 10 copies · chains A, K, B, C, E, D, F, J, L
- EOH · Ethanol · additive · 17 copies · chains B, J, G, A, C, E, H, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.31 | 0.75 | 25 | EOH, CA |
| 2 | 59 | 0.24 | 0.72 | 18 | EOH, CA |
Interfaces
15 interfaces between chains.
- B–C · 150 Ų buried · 3 hydrogen bonds · protein-protein
- A–J · 147 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 146 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 143 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 134 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 12 covalent (nonstandard, covalent ligand).
Compared structures
- 1W3M · Crystal structure of tsushimycin · 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 1W3M · PDBe 1W3M
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