MolNFT v1 · #165495 · protein
Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, datp, dcmpnpp and mg
6TXC · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, datp, dcmpnpp and mg”. X-ray diffraction, 6 ligands (0KX, GTP, DTP), 20 pockets (best…
- PDB
- 6TXC
- Type
- protein
- Length
- 7,585 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- 0KX, GTP, DTP, MG, FE, SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 14 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
| B, E, H | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 52% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
| F | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 463 | 52% helix, 14% strand | Q9Y3Z3 |
| G | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 463 | 52% helix, 14% strand | Q9Y3Z3 |
| I | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 477 | 52% helix, 13% strand | Q9Y3Z3 |
| J | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 51% helix, 13% strand | Q9Y3Z3 |
| K | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 13% strand | Q9Y3Z3 |
| L | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 475 | 52% helix, 13% strand | Q9Y3Z3 |
| M | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 471 | 52% helix, 13% strand | Q9Y3Z3 |
| N | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 475 | 52% helix, 13% strand | Q9Y3Z3 |
| O | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 465 | 52% helix, 14% strand | Q9Y3Z3 |
| P | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 461 | 52% helix, 14% strand | Q9Y3Z3 |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GTP · Guanosine-5'-triphosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 16 copies · chains A, C, D, B, E, G, H, F, I, K, L, J, M, O, P, N
- MG · Magnesium ion · metal · 42 copies · chains A, C, B, D, E, F, G, H, I, J, K, L, M, N, O, P
- FE · Fe (III) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, H, I, J, L, M
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 | 998 | 0.90 | 0.92 | 147 | GTP, DTP, MG |
| 2 | 1074 | 0.90 | 0.92 | 156 | GTP, DTP |
| 3 | 890 | 0.89 | 0.92 | 134 | DTP, GTP |
| 4 | 897 | 0.89 | 0.92 | 127 | DTP, MG, GTP |
| 5 | 715 | 0.88 | 0.92 | 116 | empty |
Interfaces
33 interfaces between chains.
- J–K · 2217 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2209 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2199 Ų buried · 26 hydrogen bonds · protein-protein
- E–H · 2124 Ų buried · 25 hydrogen bonds · protein-protein
- I–L · 2108 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6TXC · Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP… · 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 6TXC · PDBe 6TXC · UniProt Q9Y3Z3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.