Research workbench
2.4 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with DZ2002 and NAD
Analyse 2.4 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TLS
- 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
- NAD, ZD2, PO4, CL
- 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 | 496 | 46% helix, 15% strand | Q5CPH1 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 495 | 44% helix, 15% strand | Q5CPH1 |
| C, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 493 | 45% helix, 15% strand | Q5CPH1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZD2 · (2S)-4-(6-amino-9H-purin-9-yl)-2-hydroxybutanoic acid · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 17 copies · chains A, C, B, D
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.89 | 0.90 | 93 | empty |
| 2 | 620 | 0.85 | 0.90 | 69 | NAD, ZD2 |
| 3 | 634 | 0.85 | 0.89 | 72 | NAD, ZD2 |
| 4 | 599 | 0.85 | 0.90 | 70 | NAD, ZD2 |
| 5 | 604 | 0.84 | 0.89 | 70 | NAD, ZD2 |
Interfaces
6 interfaces between chains.
- C–D · 3390 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3368 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1939 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1937 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 430 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TLS · 2.4 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 5TLS · PDBe 5TLS · UniProt Q5CPH1
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