Research workbench
2.85 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with adenosine and NAD.
Analyse 2.85 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
- 5HM8
- Type
- protein
- Length
- 3,932 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q5CPH1
- Ligands
- ADN, NAD, CL, SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 494 | 45% helix, 15% strand | Q5CPH1 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 488 | 45% helix, 15% strand | Q5CPH1 |
| D, F | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 493 | 46% helix, 15% strand | Q5CPH1 |
| E | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 489 | 46% helix, 15% strand | Q5CPH1 |
| H | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 487 | 46% helix, 15% strand | Q5CPH1 |
Ligands and binding sites
- ADN · Adenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 19 copies · chains A, C, B, D, E, F, H, G
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.90 | 0.91 | 92 | empty |
| 2 | 1053 | 0.89 | 0.91 | 91 | empty |
| 3 | 582 | 0.85 | 0.91 | 68 | ADN, NAD |
| 4 | 614 | 0.85 | 0.90 | 69 | ADN, NAD |
| 5 | 627 | 0.85 | 0.90 | 69 | ADN, NAD |
Interfaces
15 interfaces between chains.
- E–F · 3365 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 3362 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 3344 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3334 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1992 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5HM8 · 2.85 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 5HM8 · PDBe 5HM8 · UniProt Q5CPH1
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