Research workbench
Crystal structure of S-adenosylmethionine-dependent methyltransferase sibl in complex with sah
Analyse Crystal structure of S-adenosylmethionine-dependent methyltransferase sibl in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X3Q
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sibl
- UniProt
- C0LTM6
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sibl | protein | 341 | 52% helix, 18% strand | C0LTM6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.87 | 0.88 | 102 | empty |
| 2 | 307 | 0.79 | 0.90 | 55 | SAH |
| 3 | 268 | 0.78 | 0.90 | 44 | SAH |
| 4 | 281 | 0.78 | 0.90 | 48 | SAH |
| 5 | 81 | 0.74 | 0.97 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3601 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3469 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 421 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4X3Q · Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex… · the same entry in another collection · chain D against D, 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 C0LTM6
- Elsewhere: RCSB PDB 4X3Q · PDBe 4X3Q · UniProt C0LTM6
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