MolNFT v1 · #78086 · protein
Crystal structure of ca bound impase family protein from staphylococcus aureus
3RYD · Inositol monophosphatase family protein: “Crystal structure of ca bound impase family protein from staphylococcus aureus”. X-ray diffraction, 3 ligands (SRT, CA, K), 5 pockets (best druggability 0.67). MolNFT v1 #78086 on GenesisL1…
- PDB
- 3RYD
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase family protein
- EC
- 3.1.3.25
- UniProt
- Q6G709
- Ligands
- SRT, CA, K
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase family protein (EC 3.1.3.25) | protein | 261 | 34% helix, 24% strand | Q6G709 |
| C | Inositol monophosphatase family protein (EC 3.1.3.25) | protein | 253 | 32% helix, 25% strand | Q6G709 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 3 copies · chains A, C
- CA · Calcium ion · metal · 3 copies · chains A, C
- K · Potassium ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.67 | 0.79 | 34 | CA, SRT |
| 2 | 345 | 0.59 | 0.77 | 40 | CA, SRT |
| 3 | 243 | 0.49 | 0.74 | 36 | empty |
| 4 | 205 | 0.45 | 0.73 | 32 | empty |
| 5 | 54 | 0.44 | 0.83 | 20 | CA |
Interfaces
1 interface between chains.
- A–C · 1398 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3RYD · Crystal structure of Ca bound IMPase family protein from Staphylococcus aureus · 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 Q6G709
- Elsewhere: RCSB PDB 3RYD · PDBe 3RYD · UniProt Q6G709
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