Research workbench
P. putida mandelate racemase co-crystallized with tartronic acid
Analyse P. putida mandelate racemase co-crystallized with tartronic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M6U
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate racemase
- EC
- 5.1.2.2
- UniProt
- P11444
- Ligands
- TTN, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mandelate racemase (EC 5.1.2.2) | protein | 357 | 40% helix, 24% strand | P11444 |
Ligands and binding sites
- TTN · Tartronate · ligand · 2 copies · chains A, B
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.74 | 0.97 | 20 | MG, TTN |
| 2 | 609 | 0.73 | 0.80 | 86 | empty |
| 3 | 72 | 0.72 | 0.96 | 20 | TTN |
| 4 | 110 | 0.50 | 0.82 | 22 | empty |
| 5 | 81 | 0.47 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1545 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 P11444
- Elsewhere: RCSB PDB 4M6U · PDBe 4M6U · UniProt P11444
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