MolNFT v1 · #64396 · protein
Crystal structure of a ld-carboxypeptidase a (SARO_1426) from novosphingobium aromaticivorans dsm at 1.89 a resolution
3G23: “Crystal structure of a ld-carboxypeptidase a (SARO_1426) from novosphingobium aromaticivorans dsm at 1.89 a…”. X-ray diffraction, 2 ligands (UNL, SO4), 3 pockets (best druggability 0.73). MolNFT v1 #64396 on GenesisL1: 3D structure…
- PDB
- 3G23
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ld-carboxypeptidase a
- UniProt
- Q2G8F3
- Ligands
- UNL, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ld-carboxypeptidase a | protein | 270 | 39% helix, 19% strand | Q2G8F3 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains A, B
- SO4 · Sulfate ion · ion · 17 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.73 | 0.78 | 75 | SO4, GOL, UNL |
| 2 | 109 | 0.45 | 0.79 | 19 | GOL |
| 3 | 54 | 0.38 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1404 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3G23 · Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium… · 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 Q2G8F3
- Elsewhere: RCSB PDB 3G23 · PDBe 3G23 · UniProt Q2G8F3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.