Research workbench
Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP-cpp
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
- 3DAY
- Type
- protein
- Length
- 535 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme a synthetase ACSM2A, mitochondrial precursor
- EC
- 6.2.1.2
- UniProt
- Q08AH3
- Ligands
- APC, MG, UNX, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-coenzyme a synthetase ACSM2A, mitochondrial precursor (EC 6.2.1.2) | protein | 535 | 33% helix, 26% strand | Q08AH3 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- UNX · Unknown atom or ion · ion · 11 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.81 | 0.82 | 108 | MG, APC, UNX |
| 2 | 100 | 0.42 | 0.78 | 23 | empty |
| 3 | 78 | 0.41 | 0.78 | 15 | GOL |
Compared structures
- 3DAY · 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 A against A, TM-score 0.84
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 3DAY · PDBe 3DAY · UniProt Q08AH3
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