Research workbench
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from geobacillus sp. Y412MC10 complexed with MAGNESIUM/TARTRATE
Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OPS
- Type
- protein
- Length
- 1,534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- D3EID5
- Ligands
- MG
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 386 | 34% helix, 26% strand | D3EID5 |
| B, C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 386 | 34% helix, 25% strand | D3EID5 |
| D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 376 | 34% helix, 26% strand | D3EID5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.74 | 0.78 | 90 | empty |
| 2 | 594 | 0.70 | 0.79 | 44 | empty |
| 3 | 835 | 0.68 | 0.75 | 59 | empty |
| 4 | 529 | 0.64 | 0.76 | 52 | empty |
| 5 | 147 | 0.55 | 0.81 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 330 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 117 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 109 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3OPS · Crystal structure of mandelate racemase/muconate lactonizing protein FROM GEOBACILLUS SP.… · 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 D3EID5
- Elsewhere: RCSB PDB 3OPS · PDBe 3OPS · UniProt D3EID5
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