Research workbench
Apo structure of CALS11, tdp-rhamnose 3'-O-methyltransferase, an enzyme in calicheamicin biosynthesis
Analyse Apo structure of CALS11, tdp-rhamnose 3'-O-methyltransferase, an enzyme in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HOQ
- Type
- protein
- Length
- 1,158 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tdp-rhamnose 3'-O-methyltransferase (CALS11)
- UniProt
- Q8KNF1
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tdp-rhamnose 3'-O-methyltransferase (CALS11) | protein | 234 | 44% helix, 15% strand | Q8KNF1 |
| B, D | Tdp-rhamnose 3'-O-methyltransferase (CALS11) | protein | 230 | 45% helix, 16% strand | Q8KNF1 |
| C | Tdp-rhamnose 3'-O-methyltransferase (CALS11) | protein | 229 | 45% helix, 16% strand | Q8KNF1 |
| E | Tdp-rhamnose 3'-O-methyltransferase (CALS11) | protein | 235 | 44% helix, 15% strand | Q8KNF1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.82 | 0.83 | 117 | SO4 |
| 2 | 390 | 0.67 | 0.80 | 43 | SO4 |
| 3 | 462 | 0.60 | 0.75 | 49 | SO4 |
| 4 | 405 | 0.60 | 0.76 | 41 | SO4 |
| 5 | 132 | 0.43 | 0.76 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2717 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 2687 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1382 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1381 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1380 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5HOQ · Apo structure of CalS11, TDP-rhamnose 3'-o-methyltransferase, an enzyme in Calicheamicin… · 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 Q8KNF1
- Elsewhere: RCSB PDB 5HOQ · PDBe 5HOQ · UniProt Q8KNF1
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