MolNFT v1 · #148611 · protein
Human methionine adenosyltransferase II mutant (S114A) in P22121 crystal form
6FBP · S-adenosylmethionine synthase isoform type-2: “Human methionine adenosyltransferase II mutant (S114A) in P22121 crystal form”. X-ray diffraction, 4 ligands (PPK, ADN, K), 8 pockets (best druggability 0.82). MolNFT v1 #148611 on…
- PDB
- 6FBP
- Type
- protein
- Length
- 754 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase isoform type-2
- EC
- 2.5.1.6
- UniProt
- P31153
- Ligands
- PPK, ADN, K, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 380 | 33% helix, 26% strand | P31153 |
| B | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 374 | 33% helix, 26% strand | P31153 |
Ligands and binding sites
- PPK · (diphosphono)aminophosphonic acid · ligand · chains A, B
- ADN · Adenosine · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.82 | 0.95 | 44 | MG, PPK, ADN |
| 2 | 435 | 0.74 | 0.83 | 37 | PG4 |
| 3 | 565 | 0.69 | 0.79 | 60 | empty |
| 4 | 82 | 0.41 | 0.78 | 11 | empty |
| 5 | 87 | 0.40 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2530 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6FBP · Human Methionine Adenosyltransferase II mutant (S114A) in P22121 crystal form · the same entry in another collection · chain A against A, TM-score 1.00
- P31153 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase isoform type-2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31153
- Elsewhere: RCSB PDB 6FBP · PDBe 6FBP · UniProt P31153
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.