Research workbench
Crystal structure of I122A/I330A variant of S-adenosylmethionine synthetase from cryptosporidium hominis in complex with onb-SAM (2- nitro benzyme S-adenosyl-methionine)
Analyse Crystal structure of I122A/I330A variant of S-adenosylmethionine synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LTV
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- A0A0S4TKQ5
- Ligands
- 3PO, EU9, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 381 | 33% helix, 26% strand | A0A0S4TKQ5 |
Ligands and binding sites
- 3PO · Triphosphate · ligand · 2 copies · chains A, B
- EU9 · [(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methyl-[(3R)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.80 | 0.85 | 71 | 3PO, MG, EU9 |
| 2 | 593 | 0.79 | 0.85 | 61 | 3PO, MG, EU9 |
| 3 | 481 | 0.72 | 0.81 | 53 | empty |
| 4 | 192 | 0.53 | 0.78 | 29 | empty |
| 5 | 146 | 0.46 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2966 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6LTV · Crystal Structure of I122A/I330A variant of S-adenosylmethionine synthetase from… · 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 A0A0S4TKQ5
- Elsewhere: RCSB PDB 6LTV · PDBe 6LTV · UniProt A0A0S4TKQ5
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