Research workbench
Crystal structure of TnmS3 in complex with tiancimycin (TNM B)
Analyse Crystal structure of TnmS3 in complex with tiancimycin (TNM B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W27
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Streptomyces sp. CB03234
- Molecule
- Glyoxalase/bleomycin resisance protein/dioxygenase
- UniProt
- A0A125SA29
- Ligands
- 9VG
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyoxalase/bleomycin resisance protein/dioxygenase | protein | 121 | 17% helix, 45% strand | A0A125SA29 |
Ligands and binding sites
- 9VG · Methyl (2E)-3-[(1as,11s,11as,14z,18r)-3,18-dihydroxy-4, 9-dioxo-4,9,10,11-tetrahydro-11AH-11,1A-hept[3]ene[1, 5]diynonaphtho[2,3-h]oxireno[c]quinolin-11A-yl]but-2-enoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.64 | 0.80 | 36 | 9VG |
| 2 | 265 | 0.62 | 0.80 | 31 | 9VG |
Interfaces
1 interface between chains.
- A–B · 1948 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5W27 · Crystal structure of TNMS3 in complex with tiancimycin (tnm B) · 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
- Every structure of UniProt A0A125SA29
- Elsewhere: RCSB PDB 5W27 · PDBe 5W27 · UniProt A0A125SA29
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