Research workbench
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from actinobacillus succinogenes 130Z complexed with MAGNESIUM/SULFATE
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
- 3N6H
- Type
- protein
- Length
- 1,711 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- A6VQF6
- Ligands
- MG, SO4, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 429 | 39% helix, 19% strand | A6VQF6 |
| B | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 432 | 39% helix, 19% strand | A6VQF6 |
| C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 426 | 38% helix, 19% strand | A6VQF6 |
| D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 424 | 38% helix, 19% strand | A6VQF6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.84 | 0.90 | 62 | empty |
| 2 | 502 | 0.81 | 0.87 | 52 | empty |
| 3 | 928 | 0.74 | 0.78 | 92 | SO4 |
| 4 | 254 | 0.69 | 0.85 | 40 | SO4 |
| 5 | 361 | 0.69 | 0.82 | 48 | SO4, MG |
Interfaces
6 interfaces between chains.
- A–B · 1393 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1373 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 784 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 751 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 3N6H · Crystal structure of Mandelate racemase/muconate lactonizing protein from Actinobacillus… · 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 A6VQF6
- Elsewhere: RCSB PDB 3N6H · PDBe 3N6H · UniProt A6VQF6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.