Research workbench
Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP
Analyse Crystal structure of human acyl-CoA synthetase medium-chain family member 2A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VZE
- Type
- protein
- Length
- 1,602 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme a synthetase ACSM2A, mitochondrial
- EC
- 6.2.1.2
- UniProt
- Q08AH3
- Ligands
- AMP, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-coenzyme a synthetase ACSM2A, mitochondrial (EC 6.2.1.2) | protein | 533 | 32% helix, 27% strand | Q08AH3 |
| C | Acyl-coenzyme a synthetase ACSM2A, mitochondrial (EC 6.2.1.2) | protein | 536 | 32% helix, 27% strand | Q08AH3 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.84 | 0.87 | 109 | AMP |
| 2 | 851 | 0.83 | 0.86 | 101 | AMP |
| 3 | 917 | 0.82 | 0.84 | 113 | AMP |
| 4 | 242 | 0.49 | 0.74 | 35 | empty |
| 5 | 84 | 0.49 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 216 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VZE · Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08AH3 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a synthetase ACSM2A, mitochondrial… · a predicted model of the same protein · chain B 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 Q08AH3
- Elsewhere: RCSB PDB 2VZE · PDBe 2VZE · UniProt Q08AH3
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