Research workbench
Human methionine adenosyltransferase II mutant (Q113A)
Analyse Human methionine adenosyltransferase II mutant (Q113A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FBN
- Type
- protein
- Length
- 741 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
- SAM, PPK, MG, K
- Pockets
- 4 · 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 | 381 | 32% helix, 26% strand | P31153 |
| B | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 360 | 33% helix, 27% strand | P31153 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A, B
- PPK · (diphosphono)aminophosphonic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, A
- K · Potassium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.82 | 0.92 | 53 | SAM, PPK, MG, K |
| 2 | 637 | 0.76 | 0.81 | 57 | EDO |
| 3 | 578 | 0.75 | 0.82 | 72 | EDO |
| 4 | 83 | 0.42 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2351 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6FBN · Human Methionine Adenosyltransferase II mutant (Q113A) · 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 6FBN · PDBe 6FBN · UniProt P31153
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