Research workbench
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing family protein from azoarcus sp. EBN1
Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing family protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QDE
- Type
- protein
- Length
- 3,000 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein
- UniProt
- Q5P025
- Ligands
- BA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein | protein | 375 | 43% helix, 18% strand | Q5P025 |
Ligands and binding sites
- BA · Barium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.87 | 0.89 | 95 | empty |
| 2 | 1083 | 0.87 | 0.88 | 103 | empty |
| 3 | 1092 | 0.87 | 0.88 | 102 | empty |
| 4 | 1039 | 0.87 | 0.88 | 97 | empty |
| 5 | 182 | 0.82 | 0.97 | 39 | empty |
Interfaces
16 interfaces between chains.
- A–H · 1300 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1291 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 1288 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1283 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1060 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2QDE · Crystal structure of mandelate racemase/muconate lactonizing family protein from Azoarcus… · 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 Q5P025
- Elsewhere: RCSB PDB 2QDE · PDBe 2QDE · UniProt Q5P025
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.