MolNFT v1 · #134585 · protein
1.95 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with adenine and NAD
5T8K: “1.95 ångström crystal structure of S-adenosylhomocysteinase from cryptosporidium parvum in complex with…”. X-ray diffraction, 3 ligands (NAD, ADE, NA), 20 pockets (best druggability 0.90). MolNFT v1 #134585 on GenesisL1: 3D…
- PDB
- 5T8K
- 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, ADE, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 491 | 46% helix, 15% strand | Q5CPH1 |
| B, C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 493 | 45% helix, 15% strand | Q5CPH1 |
| D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 493 | 46% helix, 15% strand | Q5CPH1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- ADE · Adenine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, D
- PGE · Triethylene glycol · additive · 2 copies · chains D, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 1081 | 0.90 | 0.92 | 94 | empty |
| 2 | 610 | 0.85 | 0.90 | 69 | NAD, ADE |
| 3 | 605 | 0.85 | 0.90 | 67 | NAD, ADE, P6G |
| 4 | 605 | 0.85 | 0.90 | 67 | NAD, ADE |
| 5 | 625 | 0.83 | 0.88 | 71 | NAD, ADE, PGE |
Interfaces
6 interfaces between chains.
- B–D · 3361 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3338 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1936 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1917 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 425 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 5T8K · 1.95 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 5T8K · PDBe 5T8K · UniProt Q5CPH1
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