MolNFT v1 · #160875 · protein
Structure of C. elegans ZK177.8, SAMHD1 ortholog
6PWY: “Structure of C. elegans ZK177.8, SAMHD1 ortholog”. X-ray diffraction, 3 ligands (DTP, GTP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #160875 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PWY
- Type
- protein
- Length
- 2,033 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ZK177.8
- UniProt
- Q09374
- Ligands
- DTP, GTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ZK177.8 | protein | 504 | 56% helix, 12% strand | Q09374 |
| B, C | ZK177.8 | protein | 513 | 56% helix, 11% strand | Q09374 |
| D | ZK177.8 | protein | 503 | 56% helix, 12% strand | Q09374 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 copies · chains A, B, D, C
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 6 copies · chains A, B, D, C
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 | 875 | 0.89 | 0.91 | 122 | MG, DTP, GTP |
| 2 | 932 | 0.88 | 0.91 | 129 | DTP, MG, GTP |
| 3 | 99 | 0.77 | 0.98 | 21 | empty |
| 4 | 672 | 0.70 | 0.78 | 56 | DTP |
| 5 | 647 | 0.70 | 0.78 | 60 | DTP, SIN |
Interfaces
6 interfaces between chains.
- B–C · 2073 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1939 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1781 Ų buried · 17 hydrogen bonds · protein-protein
- D–C · 1772 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 544 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q09374
- Elsewhere: RCSB PDB 6PWY · PDBe 6PWY · UniProt Q09374
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