Research workbench
2.15 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with D-eritadenine and NAD
Analyse 2.15 ångström crystal structure of S-adenosylhomocysteinase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JPI
- Type
- protein
- Length
- 1,970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q5CPH1
- Ligands
- NAD, DEA, CL, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 496 | 45% helix, 15% strand | Q5CPH1 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 491 | 46% helix, 14% strand | Q5CPH1 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 492 | 46% helix, 15% strand | Q5CPH1 |
| D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 491 | 45% helix, 14% strand | Q5CPH1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- DEA · D-eritadenine · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains B, C
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.88 | 0.91 | 74 | empty |
| 2 | 627 | 0.85 | 0.90 | 74 | NAD, DEA |
| 3 | 646 | 0.85 | 0.89 | 70 | NAD, DEA |
| 4 | 678 | 0.84 | 0.88 | 77 | NAD, DEA |
| 5 | 668 | 0.84 | 0.88 | 79 | NAD, DEA |
Interfaces
6 interfaces between chains.
- A–B · 3366 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 3318 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1921 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1912 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 426 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5JPI · 2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum… · 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 Q5CPH1
- Elsewhere: RCSB PDB 5JPI · PDBe 5JPI · UniProt Q5CPH1
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