Research workbench
Crystal structure of putative mandelate RACEMASE/MUCONATE lactonizing protein from clostridium beijerinckii ncimb 8052
Analyse Crystal structure of putative mandelate RACEMASE/MUCONATE lactonizing protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GY1
- Type
- protein
- Length
- 775 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- A6M2W4
- Ligands
- MG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 387 | 41% helix, 20% strand | A6M2W4 |
| B | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 388 | 41% helix, 20% strand | A6M2W4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.69 | 0.79 | 49 | empty |
| 2 | 511 | 0.68 | 0.79 | 42 | empty |
| 3 | 381 | 0.67 | 0.80 | 35 | empty |
| 4 | 362 | 0.67 | 0.80 | 39 | empty |
| 5 | 64 | 0.58 | 0.89 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2751 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3GY1 · CRYSTAL STRUCTURE OF putative mandelate racemase/muconate lactonizing protein from… · the same entry in another collection · chain A against A, TM-score 1.00
- A6M2W4 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member CBEI_4837… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A6M2W4
- Elsewhere: RCSB PDB 3GY1 · PDBe 3GY1 · UniProt A6M2W4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.