Research workbench
Crystal structure of TNMS3 in complex with tnm C
Analyse Crystal structure of TNMS3 in complex with tnm C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BBX
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLYOXALASE/BLEOMYCIN resisance PROTEIN/DIOXYGENASE
- UniProt
- A0A125SA29
- Ligands
- D77
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GLYOXALASE/BLEOMYCIN resisance PROTEIN/DIOXYGENASE | protein | 121 | 17% helix, 43% strand | A0A125SA29 |
Ligands and binding sites
- D77 · methyl (2R,3R)-2,3-dihydroxy-3-[(1aS,11S,11aR,14Z,18R)-3,7,8,18-tetrahydroxy-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]butanoate · 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 | 277 | 0.62 | 0.80 | 30 | D77 |
| 2 | 268 | 0.62 | 0.80 | 32 | D77 |
Interfaces
1 interface between chains.
- A–B · 1961 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6BBX · Crystal structure of TnmS3 in complex with TNM C · 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 6BBX · PDBe 6BBX · UniProt A0A125SA29
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