MolNFT v1 · #123871 · protein
2.25 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with neplanocin-a and NAD
5JXW: “2.25 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with…”. X-ray diffraction, 2 ligands (6OS, NAD), 20 pockets (best druggability 0.88). MolNFT v1 #123871 on GenesisL1: 3D structure…
- PDB
- 5JXW
- Type
- protein
- Length
- 1,949 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
- 6OS, NAD
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 486 | 44% helix, 15% strand | Q5CPH1 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 486 | 45% helix, 15% strand | Q5CPH1 |
| D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 491 | 45% helix, 15% strand | Q5CPH1 |
Ligands and binding sites
- 6OS · Neplanocin-A · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B, C, D
- P6G · Hexaethylene glycol · additive · 2 copies · chains B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.88 | 0.90 | 91 | empty |
| 2 | 588 | 0.85 | 0.91 | 68 | 6OS, NAD |
| 3 | 611 | 0.84 | 0.89 | 72 | 6OS, NAD |
| 4 | 582 | 0.84 | 0.90 | 71 | 6OS, NAD |
| 5 | 612 | 0.84 | 0.89 | 67 | 6OS, NAD |
Interfaces
6 interfaces between chains.
- A–B · 3354 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3353 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1919 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1912 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 433 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5JXW · 2.25 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 5JXW · PDBe 5JXW · UniProt Q5CPH1
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