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Crystal structure of S-adenosylmethionine synthetase (METK/MAT) from cryptosporidium parvum
Analyse Crystal structure of S-adenosylmethionine synthetase (METK/MAT) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C07
- Type
- protein
- Length
- 1,486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- Q5CYE4
- Ligands
- MG, K, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 376 | 33% helix, 26% strand | Q5CYE4 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 368 | 33% helix, 27% strand | Q5CYE4 |
| C | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 374 | 33% helix, 27% strand | Q5CYE4 |
| D | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 368 | 33% helix, 27% strand | Q5CYE4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- K · Potassium ion · metal · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.78 | 0.80 | 90 | empty |
| 2 | 762 | 0.73 | 0.79 | 76 | K, MG |
| 3 | 466 | 0.73 | 0.82 | 48 | empty |
| 4 | 407 | 0.73 | 0.83 | 46 | empty |
| 5 | 523 | 0.72 | 0.81 | 66 | MG |
Interfaces
3 interfaces between chains.
- C–D · 2400 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2315 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 985 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6C07 · Crystal Structure of S-Adenosylmethionine synthetase (MetK/Mat) from Cryptosporidium… · 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 Q5CYE4
- Elsewhere: RCSB PDB 6C07 · PDBe 6C07 · UniProt Q5CYE4
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