Research workbench
Crystal structure of methionine adenosyltransferase from pyrococcus furiosus in complex with amppcp, SAM, and pcp
Analyse Crystal structure of methionine adenosyltransferase from pyrococcus furiosus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S83
- Type
- protein
- Length
- 3,200 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- Q8TZW1
- Ligands
- MDN, ACP, SAM, MG, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 400 | 38% helix, 29% strand | Q8TZW1 |
Ligands and binding sites
- MDN · Methylenediphosphonic acid · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B, E, F
- MG · Magnesium ion · metal · 21 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.81 | 0.92 | 54 | MDN, MG, SAM, PO4 |
| 2 | 573 | 0.79 | 0.85 | 68 | MDN, MG, SAM, PO4 |
| 3 | 402 | 0.78 | 0.87 | 59 | empty |
| 4 | 165 | 0.78 | 0.95 | 25 | empty |
| 5 | 440 | 0.78 | 0.86 | 60 | empty |
Interfaces
14 interfaces between chains.
- E–F · 3107 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3054 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 2802 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2749 Ų buried · 42 hydrogen bonds · protein-protein
- E–H · 1185 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6S83 · Crystal structure of methionine adenosyltransferase from Pyrococcus furiosus in complex… · the same entry in another collection · chain E against E, TM-score 1.00
- Q8TZW1 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q8TZW1) · a predicted model of the same protein · chain H 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 Q8TZW1
- Elsewhere: RCSB PDB 6S83 · PDBe 6S83 · UniProt Q8TZW1
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