MolNFT v1 · #134919 · protein
2.6 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with aristeromycin and NAD
5TJ9: “2.6 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with…”. X-ray diffraction, 3 ligands (7CY, NAD, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #134919 on GenesisL1: 3D…
- PDB
- 5TJ9
- Type
- protein
- Length
- 1,977 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
- 7CY, NAD, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 493 | 45% helix, 15% strand | Q5CPH1 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 494 | 45% helix, 15% strand | Q5CPH1 |
| C, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 495 | 45% helix, 15% strand | Q5CPH1 |
Ligands and binding sites
- 7CY · (1R,2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)cyclopentane-1,2-diol · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains D, C
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.89 | 0.90 | 94 | empty |
| 2 | 635 | 0.85 | 0.90 | 72 | 7CY, NAD, P6G |
| 3 | 1162 | 0.84 | 0.85 | 114 | 7CY, NAD |
| 4 | 1048 | 0.84 | 0.85 | 109 | 7CY, NAD, PEG |
| 5 | 617 | 0.84 | 0.89 | 72 | 7CY, NAD |
Interfaces
6 interfaces between chains.
- C–D · 3340 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3310 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1935 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1922 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 426 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5TJ9 · 2.6 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in… · 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 5TJ9 · PDBe 5TJ9 · UniProt Q5CPH1
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