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Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dampnpp and mg
Analyse Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XU1
- Type
- protein
- Length
- 3,816 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- DZ4, GTP, MG, FE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 52% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 52% helix, 13% strand | Q9Y3Z3 |
| D, H | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 52% helix, 13% strand | Q9Y3Z3 |
| E | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 464 | 52% helix, 14% strand | Q9Y3Z3 |
| F | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 13% strand | Q9Y3Z3 |
| G | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 53% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 16 copies · chains A, C, D, B, E, G, H, F
- GTP · Guanosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 25 copies · chains A, C, B, D, E, G, F, H
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 982 | 0.87 | 0.88 | 104 | MG, GTP, DZ4 |
| 2 | 876 | 0.86 | 0.88 | 99 | DZ4, MG, GTP |
| 3 | 772 | 0.86 | 0.89 | 86 | DZ4, MG, GTP |
| 4 | 755 | 0.86 | 0.89 | 90 | MG, GTP, DZ4 |
| 5 | 765 | 0.86 | 0.89 | 93 | GTP, MG, DZ4 |
Interfaces
17 interfaces between chains.
- F–G · 2141 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2130 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2128 Ų buried · 33 hydrogen bonds · protein-protein
- E–H · 1955 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1869 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6XU1 · Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dAMPNPP… · 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 6XU1 · PDBe 6XU1 · UniProt Q9Y3Z3
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