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The enolisation chemistry of a thioester-dependent racemase: the 1.4 a crystal structure of a complex with a planar reaction intermediate analogue
Analyse The enolisation chemistry of a thioester-dependent racemase: the 1.4 a crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YIM
- Type
- protein
- Length
- 1,420 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable alpha-methylacyl-CoA racemase mcr (2-methylacyl-CoA racemase)…
- EC
- 5.1.99.4
- UniProt
- O06543
- Ligands
- MC4, PO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable alpha-methylacyl-CoA racemase mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) (EC 5.1.99.4) | protein | 355 | 41% helix, 15% strand | O06543 |
Ligands and binding sites
- MC4 · 2-methylacetoacetyl coa · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, A, D
- GOL · Glycerol · 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 | 560 | 0.71 | 0.80 | 60 | MC4 |
| 2 | 451 | 0.71 | 0.81 | 59 | MC4 |
| 3 | 521 | 0.70 | 0.80 | 58 | MC4 |
| 4 | 441 | 0.70 | 0.81 | 60 | MC4 |
| 5 | 514 | 0.60 | 0.74 | 59 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6483 Ų buried · 103 hydrogen bonds · protein-protein
- C–D · 6412 Ų buried · 102 hydrogen bonds · protein-protein
- A–D · 327 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2YIM · The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure… · the same entry in another collection · chain D against D, TM-score 1.00
- O06543 · AlphaFold monomer V2.0 prediction for alpha-methylacyl-CoA racemase (O06543) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O06543
- Elsewhere: RCSB PDB 2YIM · PDBe 2YIM · UniProt O06543
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