MolNFT v1 · #163607 · protein
Crystal structure of methionine adenosyltransferase from pyrococcus furiosus in complex with amppcp, SAM, and pcp
6S83 · S-adenosylmethionine synthase: “Crystal structure of methionine adenosyltransferase from pyrococcus furiosus in complex with amppcp, SAM, and…”. X-ray diffraction, 5 ligands (MDN, ACP, SAM), 20 pockets (best druggability 0.81).…
- 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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