MolNFT v1 · #49896 · protein
Structure of a quorum-quenching lactonase (aiib) from agrobacterium tumefaciens
2R2D · Zn-dependent hydrolases: “Structure of a quorum-quenching lactonase (aiib) from agrobacterium tumefaciens”. X-ray diffraction, 2 ligands (ZN, PO4), 14 pockets (best druggability 0.82). MolNFT v1 #49896 on GenesisL1: 3D structure…
- PDB
- 2R2D
- Type
- protein
- Length
- 1,656 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zn-dependent hydrolases
- UniProt
- A9CKY2
- Ligands
- ZN, PO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Zn-dependent hydrolases | protein | 276 | 25% helix, 26% strand | A9CKY2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.82 | 0.83 | 97 | PO4, GOL |
| 2 | 276 | 0.67 | 0.83 | 34 | PO4, GOL |
| 3 | 254 | 0.66 | 0.83 | 30 | PO4, GOL |
| 4 | 239 | 0.65 | 0.83 | 31 | PO4, GOL |
| 5 | 263 | 0.64 | 0.81 | 31 | PO4, GOL |
Interfaces
7 interfaces between chains.
- B–C · 1134 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 214 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 188 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 180 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 97 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2R2D · Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens · the same entry in another collection · chain F against F, TM-score 1.00
- A9CKY2 · AlphaFold monomer V2.0 prediction for N-acyl homoserine lactonase aiib (A9CKY2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A9CKY2
- Elsewhere: RCSB PDB 2R2D · PDBe 2R2D · UniProt A9CKY2
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