MolNFT v1 · #107167 · protein
Crystal structure of S-adenosylmethionine-dependent methyltransferase sibl in complex with 3HK and sah
4U1Q: “Crystal structure of S-adenosylmethionine-dependent methyltransferase sibl in complex with 3HK and sah”. X-ray diffraction, 2 ligands (3DJ, SAH), 16 pockets (best druggability 0.88). MolNFT v1 #107167 on GenesisL1: 3D structure…
- PDB
- 4U1Q
- 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
- 3DJ, SAH
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sibl | protein | 341 | 53% helix, 17% strand | C0LTM6 |
Ligands and binding sites
- 3DJ · (2S)-2-amino-4-(2-amino-3-hydroxyphenyl)-4-oxobutanoic acid · ligand · 4 copies · chains A, B, C, D
- 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
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.88 | 0.90 | 109 | empty |
| 2 | 240 | 0.79 | 0.92 | 42 | 3DJ, SAH |
| 3 | 247 | 0.78 | 0.90 | 42 | 3DJ, SAH |
| 4 | 322 | 0.75 | 0.87 | 52 | 3DJ, SAH |
| 5 | 272 | 0.74 | 0.87 | 46 | 3DJ, SAH |
Interfaces
6 interfaces between chains.
- A–B · 3581 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 3564 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 409 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4U1Q · Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex… · the same entry in another collection · chain B against B, 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 4U1Q · PDBe 4U1Q · UniProt C0LTM6
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