Research workbench
The structure of nucleotide phosphatase SA1684 complex with GDP analogue from staphylococcus aureus
Analyse The structure of nucleotide phosphatase SA1684 complex with GDP analogue from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D8Q
- Type
- protein
- Length
- 174 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0374 protein SAB1800C
- UniProt
- Q2YU19
- Ligands
- GZF, MG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0374 protein SAB1800C | protein | 174 | 28% helix, 43% strand | Q2YU19 |
Ligands and binding sites
- GZF · [(2R,3R,4S,5S)-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl) phosphinothioyl hydrogen phosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.55 | 0.80 | 30 | empty |
| 2 | 54 | 0.35 | 0.78 | 13 | empty |
Compared structures
- 7D8Q · The structure of nucleotide phosphatase Sa1684 complex with GDP analogue from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YU19 · AlphaFold monomer V2.0 prediction for UPF0374 protein SAB1800C (Q2YU19) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q2YU19
- Elsewhere: RCSB PDB 7D8Q · PDBe 7D8Q · UniProt Q2YU19
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