MolNFT v1 · #165493 · protein
Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with xtp, dgmpnpp and mg
6TXA · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with xtp, dgmpnpp and mg”. X-ray diffraction, 5 ligands (XG4, CZF, MG), 20 pockets (best druggability…
- PDB
- 6TXA
- Type
- protein
- Length
- 7,666 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
- XG4, CZF, MG, FE, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 13 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| B, E | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 53% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 53% helix, 13% strand | Q9Y3Z3 |
| F, P | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 52% helix, 13% strand | Q9Y3Z3 |
| G | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 52% helix, 13% strand | Q9Y3Z3 |
| I | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 53% helix, 13% strand | Q9Y3Z3 |
| J | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 53% helix, 13% strand | Q9Y3Z3 |
| K | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 53% helix, 13% strand | Q9Y3Z3 |
| L | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 54% helix, 13% strand | Q9Y3Z3 |
| M | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 476 | 54% helix, 13% strand | Q9Y3Z3 |
| N | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 477 | 53% helix, 13% strand | Q9Y3Z3 |
| O | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 486 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · 32 copies · chains A, C, D, B, E, G, H, F, I, J, L, K, M, O, P, N
- CZF · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- MG · Magnesium ion · metal · 48 copies · chains A, C, B, D, E, G, F, 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 · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
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 | 1013 | 0.89 | 0.91 | 135 | CZF, XG4 |
| 2 | 1014 | 0.89 | 0.91 | 144 | XG4, MG, CZF |
| 3 | 934 | 0.89 | 0.91 | 122 | XG4, MG, CZF |
| 4 | 1190 | 0.89 | 0.90 | 145 | CZF, XG4 |
| 5 | 658 | 0.85 | 0.90 | 87 | CZF, XG4 |
Interfaces
35 interfaces between chains.
- J–K · 2152 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2145 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2142 Ų buried · 31 hydrogen bonds · protein-protein
- E–H · 2138 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 2120 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6TXA · Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP… · 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 6TXA · PDBe 6TXA · UniProt Q9Y3Z3
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