Research workbench
Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit
Analyse Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YDX
- Type
- protein
- Length
- 1,560 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine adenosyltransferase 2 subunit beta
- UniProt
- Q9NZL9
- Ligands
- STL, NAP, TXP, CA, SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Methionine adenosyltransferase 2 subunit beta | protein | 312 | 42% helix, 16% strand | Q9NZL9 |
Ligands and binding sites
- STL · Resveratrol · ligand · 10 copies · chains A, C, B, D, E
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TXP · 1,4,5,6-tetrahydronicotinamide adenine dinucleotide phosphate · ligand · chains E
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 19 copies · chains A, C, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.77 | 0.83 | 54 | STL, NAP, SO4 |
| 2 | 788 | 0.77 | 0.81 | 63 | STL, NAP, SO4 |
| 3 | 629 | 0.76 | 0.82 | 61 | STL, NAP, SO4 |
| 4 | 656 | 0.76 | 0.81 | 57 | STL, NAP, SO4 |
| 5 | 579 | 0.75 | 0.82 | 53 | STL, TXP, SO4 |
Interfaces
5 interfaces between chains.
- D–E · 1083 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1033 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 621 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 55 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YDX · Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZL9 · AlphaFold monomer V2.0 prediction for methionine adenosyltransferase 2 subunit beta… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9NZL9
- Elsewhere: RCSB PDB 2YDX · PDBe 2YDX · UniProt Q9NZL9
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