Research workbench
2.25 ångström resolution crystal structure of fatty-acid-CoA ligase (FADD32) from mycobacterium smegmatis in complex with inhibitor 5'-O- [(11-PHENOXYUNDECANOYL)SULFAMOYL]ADENOSINE.
Analyse 2.25 ångström resolution crystal structure of fatty-acid-CoA ligase (FADD32)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICR
- Type
- protein
- Length
- 2,443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA synthase
- UniProt
- A0R618
- Ligands
- 649, SO4, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA synthase | protein | 607 | 33% helix, 26% strand | A0R618 |
| B | Acyl-CoA synthase | protein | 609 | 35% helix, 26% strand | A0R618 |
| C | Acyl-CoA synthase | protein | 618 | 34% helix, 25% strand | A0R618 |
| D | Acyl-CoA synthase | protein | 609 | 33% helix, 26% strand | A0R618 |
Ligands and binding sites
- 649 · 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.89 | 0.91 | 173 | 649 |
| 2 | 657 | 0.88 | 0.92 | 103 | 649 |
| 3 | 686 | 0.87 | 0.92 | 103 | 649 |
| 4 | 892 | 0.86 | 0.88 | 117 | 649 |
| 5 | 744 | 0.84 | 0.88 | 76 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1347 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1283 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 307 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ICR · 2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from… · the same entry in another collection · chain D against D, TM-score 1.00
- A0R618 · AlphaFold monomer V2.0 prediction for long-chain-fatty-acid--AMP ligase FADD32 (A0R618) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A0R618
- Elsewhere: RCSB PDB 5ICR · PDBe 5ICR · UniProt A0R618
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.