Research workbench
Crystal structure of lipate-protein ligase a from escherichia COLI complexed with lipoic acid
Analyse Crystal structure of lipate-protein ligase a from escherichia COLI complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X2H
- Type
- protein
- Length
- 997 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoate-protein ligase a
- EC
- 6.3.2.-
- UniProt
- P32099
- Ligands
- LPA
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipoate-protein ligase a (EC 6.3.2.-) | protein | 330 | 34% helix, 28% strand | P32099 |
| C | Lipoate-protein ligase a (EC 6.3.2.-) | protein | 337 | 32% helix, 26% strand | P32099 |
Ligands and binding sites
- LPA · Lipoic acid · ligand · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.83 | 0.92 | 49 | empty |
| 2 | 241 | 0.74 | 0.89 | 38 | empty |
| 3 | 159 | 0.74 | 0.92 | 34 | empty |
| 4 | 490 | 0.72 | 0.81 | 46 | LPA |
| 5 | 523 | 0.70 | 0.80 | 48 | LPA |
Interfaces
3 interfaces between chains.
- A–C · 2233 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1139 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 1X2H · Crystal Structure of Lipate-Protein Ligase A from Escherichia coli complexed with lipoic… · the same entry in another collection · chain A against A, TM-score 1.00
- P32099 · AlphaFold monomer V2.0 prediction for lipoate-protein ligase a (P32099) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P32099
- Elsewhere: RCSB PDB 1X2H · PDBe 1X2H · UniProt P32099
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