MolNFT v1 · #120738 · protein
Crystal structure of a thermostable methionine adenosyltransferase
5H9U · S-adenosylmethionine synthase: “Crystal structure of a thermostable methionine adenosyltransferase”. X-ray diffraction, 17 pockets (best druggability 0.79). MolNFT v1 #120738 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5H9U
- Type
- protein
- Length
- 1,576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- Q72I53
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 394 | 35% helix, 24% strand | Q72I53 |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.79 | 0.81 | 84 | empty |
| 2 | 862 | 0.78 | 0.81 | 81 | empty |
| 3 | 922 | 0.77 | 0.80 | 88 | empty |
| 4 | 600 | 0.76 | 0.83 | 66 | empty |
| 5 | 767 | 0.76 | 0.81 | 68 | empty |
Interfaces
6 interfaces between chains.
- C–A · 2619 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 2608 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 452 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 408 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5H9U · Crystal structure of a thermostable methionine adenosyltransferase · the same entry in another collection · chain C against C, TM-score 1.00
- Q72I53 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q72I53) · a predicted model of the same protein · chain C 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 Q72I53
- Elsewhere: RCSB PDB 5H9U · PDBe 5H9U · UniProt Q72I53
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