Research workbench
Crystal structure of CALS11, calicheamicin methyltransferase
Analyse Crystal structure of CALS11, calicheamicin methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TOS
- Type
- protein
- Length
- 2,517 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALS11
- UniProt
- Q8KNF1
- Ligands
- SAH, GLU, NA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, H, I, J | CALS11 | protein | 251 | 43% helix, 14% strand | Q8KNF1 |
| B | CALS11 | protein | 257 | 42% helix, 14% strand | Q8KNF1 |
| G | CALS11 | protein | 252 | 42% helix, 14% strand | Q8KNF1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- GLU · Glutamic acid · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.86 | 0.87 | 132 | SAH, GLU, NA, EDO |
| 2 | 1198 | 0.86 | 0.87 | 136 | SAH, GLU, NA, EDO |
| 3 | 572 | 0.83 | 0.89 | 90 | SAH, GLU, NA, EDO |
| 4 | 1029 | 0.83 | 0.84 | 103 | GLU, NA, EDO, SAH |
| 5 | 497 | 0.83 | 0.90 | 70 | SAH, GLU, NA, EDO |
Interfaces
20 interfaces between chains.
- A–D · 2709 Ų buried · 20 hydrogen bonds · protein-protein
- E–I · 2698 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2698 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 2695 Ų buried · 20 hydrogen bonds · protein-protein
- H–J · 2686 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3TOS · Crystal Structure of CalS11, Calicheamicin Methyltransferase · the same entry in another collection · chain E against E, 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 3TOS · PDBe 3TOS · UniProt Q8KNF1
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