MolNFT v1 · #162825 · protein
Inter-dimeric interface controls function and stability of S- methionine adenosyltransferase from U. urealiticum
6RKA: “Inter-dimeric interface controls function and stability of S- methionine adenosyltransferase from U.…”. X-ray diffraction, 3 ligands (ATP, SAM, PO4), 19 pockets (best druggability 0.84). MolNFT v1 #162825 on GenesisL1: 3D structure…
- PDB
- 6RKA
- Type
- protein
- Length
- 1,470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine adenosyltransferase
- EC
- 2.5.1.6
- UniProt
- B2NE58
- Ligands
- ATP, SAM, PO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 373 | 34% helix, 23% strand | B2NE58 |
| B | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 360 | 33% helix, 24% strand | B2NE58 |
| C | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 375 | 34% helix, 23% strand | B2NE58 |
| D | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 362 | 33% helix, 24% strand | B2NE58 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.84 | 0.96 | 46 | SAM, PO4 |
| 2 | 241 | 0.83 | 0.95 | 43 | SAM, ATP |
| 3 | 818 | 0.73 | 0.78 | 85 | empty |
| 4 | 636 | 0.73 | 0.80 | 62 | PO4 |
| 5 | 777 | 0.73 | 0.78 | 60 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2717 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2525 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 313 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 275 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6RKA · Inter-dimeric interface controls function and stability of S-methionine… · the same entry in another collection · chain A against A, TM-score 1.00
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 B2NE58
- Elsewhere: RCSB PDB 6RKA · PDBe 6RKA · UniProt B2NE58
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