MolNFT v1 · #162827 · protein
Inter-dimeric interface controls function and stability of S- methionine adenosyltransferase from U. urealiticum
6RKC: “Inter-dimeric interface controls function and stability of S- methionine adenosyltransferase from U.…”. X-ray diffraction, 4 ligands (SAM, PPK, MG), 20 pockets (best druggability 0.85). MolNFT v1 #162827 on GenesisL1: 3D structure…
- PDB
- 6RKC
- Type
- protein
- Length
- 2,982 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine adenosyltransferase
- EC
- 2.5.1.6
- UniProt
- B2NE58
- Ligands
- SAM, PPK, MG, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, H | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 372 | 35% helix, 24% strand | B2NE58 |
| B, F | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 374 | 33% helix, 24% strand | B2NE58 |
| C, G | Methionine adenosyltransferase (EC 2.5.1.6) | protein | 373 | 34% helix, 24% strand | B2NE58 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 16 copies · chains A, B, D, C, E, F, H, G
- PPK · (diphosphono)aminophosphonic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 7 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.85 | 0.95 | 45 | MG, K, PPK, SAM |
| 2 | 289 | 0.84 | 0.95 | 48 | K, MG, SAM, PPK |
| 3 | 276 | 0.84 | 0.95 | 46 | MG, PPK, SAM |
| 4 | 277 | 0.83 | 0.95 | 47 | K, MG, SAM, PPK |
| 5 | 271 | 0.83 | 0.95 | 47 | MG, K, PPK, SAM |
Interfaces
14 interfaces between chains.
- G–H · 3129 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3075 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 2998 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2963 Ų buried · 55 hydrogen bonds · protein-protein
- F–G · 660 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RKC · Inter-dimeric interface controls function and stability of S-methionine… · the same entry in another collection · chain D against D, 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 6RKC · PDBe 6RKC · UniProt B2NE58
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