Research workbench
Crystal structure of enolase BRADO_4202 (target efi-501651) from bradyrhizobium complexed with magnesium and mandelic acid
Analyse Crystal structure of enolase BRADO_4202 (target efi-501651) from bradyrhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TTE
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- EC
- 5.1.2.2, 5.5.1.1
- UniProt
- A4YVM8
- Ligands
- SMN, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 5.1.2.2, 5.5.1.1) | protein | 361 | 41% helix, 22% strand | A4YVM8 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 5.1.2.2, 5.5.1.1) | protein | 359 | 42% helix, 20% strand | A4YVM8 |
Ligands and binding sites
- SMN · (S)-mandelic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.77 | 0.83 | 62 | empty |
| 2 | 231 | 0.66 | 0.83 | 37 | empty |
| 3 | 214 | 0.56 | 0.79 | 33 | SMN |
| 4 | 151 | 0.52 | 0.79 | 27 | FMT |
| 5 | 150 | 0.51 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 993 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3TTE · Crystal structure of enolase brado_4202 (target EFI-501651) from Bradyrhizobium complexed… · 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 A4YVM8
- Elsewhere: RCSB PDB 3TTE · PDBe 3TTE · UniProt A4YVM8
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