Research workbench
Crystal structure of the tetrameric dgtp-bound wild type SAMHD1 catalytic core
Analyse Crystal structure of the tetrameric dgtp-bound wild type SAMHD1 catalytic core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BZC
- Type
- protein
- Length
- 1,904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- T8T, MN, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 476 | 52% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 477 | 52% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 53% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 470 | 53% helix, 14% strand | Q9Y3Z3 |
Ligands and binding sites
- T8T · 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) · ligand · 12 copies · chains A, C, D, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.90 | 0.92 | 125 | T8T, MG |
| 2 | 882 | 0.86 | 0.88 | 97 | T8T, MG |
| 3 | 631 | 0.85 | 0.89 | 79 | T8T, MG |
| 4 | 422 | 0.82 | 0.90 | 59 | T8T, MG |
| 5 | 132 | 0.82 | 0.99 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2256 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2142 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1997 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1897 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 489 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BZC · Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core · 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 Q9Y3Z3
- Elsewhere: RCSB PDB 4BZC · PDBe 4BZC · UniProt Q9Y3Z3
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