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Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from a marine actinobacterium
Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MSY
- Type
- protein
- Length
- 2,107 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- EC
- 5.5.1.1
- UniProt
- A4AFX2
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 5.5.1.1) | protein | 349 | 41% helix, 21% strand | A4AFX2 |
| B, D, F | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 5.5.1.1) | protein | 351 | 41% helix, 21% strand | A4AFX2 |
| C | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 5.5.1.1) | protein | 355 | 42% helix, 22% strand | A4AFX2 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 5.5.1.1) | protein | 350 | 41% helix, 20% strand | A4AFX2 |
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.89 | 0.90 | 122 | empty |
| 2 | 369 | 0.86 | 0.95 | 41 | empty |
| 3 | 361 | 0.86 | 0.95 | 40 | empty |
| 4 | 1062 | 0.86 | 0.87 | 106 | empty |
| 5 | 347 | 0.86 | 0.95 | 42 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1208 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1196 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1095 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1094 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 3MSY · Crystal Structure of Mandelate racemase/muconate lactonizing enzyme from a Marine… · 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 A4AFX2
- Elsewhere: RCSB PDB 3MSY · PDBe 3MSY · UniProt A4AFX2
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