Research workbench
The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an ASPARTATE/HISTIDINE pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety
Analyse The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GD2
- Type
- protein
- Length
- 1,416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable alpha-methylacyl-CoA racemase mcr
- EC
- 5.1.99.4
- Ligands
- CAA
- Pockets
- 11 · 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 (EC 5.1.99.4) | protein | 354 | 41% helix, 15% strand | — |
Ligands and binding sites
- CAA · Acetoacetyl-coenzyme A · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.71 | 0.79 | 62 | CAA, GOL |
| 2 | 552 | 0.71 | 0.79 | 69 | CAA, GOL |
| 3 | 475 | 0.70 | 0.81 | 57 | CAA |
| 4 | 515 | 0.70 | 0.79 | 58 | CAA |
| 5 | 524 | 0.61 | 0.75 | 61 | empty |
Interfaces
3 interfaces between chains.
- C–D · 6424 Ų buried · 106 hydrogen bonds · protein-protein
- A–B · 6381 Ų buried · 108 hydrogen bonds · protein-protein
- A–D · 319 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2GD2 · The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed… · 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
- Elsewhere: RCSB PDB 2GD2 · PDBe 2GD2
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