Research workbench
2.25 ångström resolution crystal structure of long-chain-fatty-acid- AMP ligase FADD32 from mycobacterium tuberculosis in complex with inhibitor 5'-O-[(11-PHENOXYUNDECANOYL)SULFAMOYL]ADENOSINE
Analyse 2.25 ångström resolution crystal structure of long-chain-fatty-acid- AMP ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HM3
- Type
- protein
- Length
- 625 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Long-chain-fatty-acid--AMP ligase FADD32
- EC
- 6.2.1.-
- UniProt
- O53580
- Ligands
- 649, PO4, CL
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Long-chain-fatty-acid--AMP ligase FADD32 (EC 6.2.1.-) | protein | 625 | 31% helix, 25% strand | O53580 |
Ligands and binding sites
- 649 · 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.87 | 0.88 | 110 | 649, PO4, PEG, GOL |
| 2 | 144 | 0.70 | 0.89 | 24 | empty |
| 3 | 162 | 0.50 | 0.78 | 35 | empty |
| 4 | 103 | 0.39 | 0.76 | 18 | empty |
| 5 | 95 | 0.36 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 5 modified (engineered, artifact).
Compared structures
- 5HM3 · 2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-acid-AMP Ligase FadD32… · the same entry in another collection · chain A against A, TM-score 1.00
- O53580 · AlphaFold monomer V2.0 prediction for long-chain-fatty-acid--AMP ligase FADD32 (O53580) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O53580
- Elsewhere: RCSB PDB 5HM3 · PDBe 5HM3 · UniProt O53580
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