MolNFT v1 · #106362 · protein
Crystal structure of L. monocytogenes psta in complex with cyclic-di- AMP
4RWW · LMO2692 protein: “Crystal structure of L. monocytogenes psta in complex with cyclic-di- AMP”. X-ray diffraction, 1 ligand (2BA), 3 pockets (best druggability 0.65). MolNFT v1 #106362 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RWW
- Type
- protein
- Length
- 322 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO2692 protein
- UniProt
- Q8Y3Y7
- Ligands
- 2BA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO2692 protein | protein | 113 | 24% helix, 38% strand | Q8Y3Y7 |
| B | LMO2692 protein | protein | 106 | 25% helix, 41% strand | Q8Y3Y7 |
| C | LMO2692 protein | protein | 103 | 26% helix, 42% strand | Q8Y3Y7 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.65 | 0.79 | 40 | 2BA |
| 2 | 330 | 0.63 | 0.79 | 38 | 2BA |
| 3 | 321 | 0.63 | 0.79 | 40 | 2BA |
Interfaces
3 interfaces between chains.
- A–C · 1205 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1137 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1096 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4RWW · Crystal Structure of L. monocytogenes PstA in complex with cyclic-di-AMP · 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 Q8Y3Y7
- Elsewhere: RCSB PDB 4RWW · PDBe 4RWW · UniProt Q8Y3Y7
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