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Crystal structure of a mandelate RACEMASE/MUCONATE lactonizing enzyme- like protein from rubrobacter xylanophilus
Analyse Crystal structure of a mandelate RACEMASE/MUCONATE lactonizing enzyme- like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CYJ
- Type
- protein
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein
- UniProt
- Q1ASJ4
- Ligands
- NA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein | protein | 359 | 43% helix, 25% strand | Q1ASJ4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.83 | 0.84 | 113 | empty |
| 2 | 1050 | 0.83 | 0.84 | 99 | empty |
| 3 | 54 | 0.73 | 0.99 | 17 | empty |
| 4 | 239 | 0.72 | 0.87 | 35 | GOL |
| 5 | 252 | 0.71 | 0.87 | 34 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 1378 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1361 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1193 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3CYJ · Crystal structure of a mandelate racemase/muconate lactonizing enzyme-like protein from… · 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 Q1ASJ4
- Elsewhere: RCSB PDB 3CYJ · PDBe 3CYJ · UniProt Q1ASJ4
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