MolNFT v1 · #57426 · protein
Crystal structure of E. COLI lipoate-protein ligase a in complex with octyl-AMP and apoh-protein
3A7A: “Crystal structure of E. COLI lipoate-protein ligase a in complex with octyl-AMP and apoh-protein”. X-ray diffraction, 1 ligand (AMP), 7 pockets (best druggability 0.79). MolNFT v1 #57426 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3A7A
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoate-protein ligase a; Glycine cleavage system H protein
- EC
- 6.3.4.-
- UniProt
- P32099, P0A6T9
- Ligands
- AMP
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lipoate-protein ligase a (EC 6.3.4.-) | protein | 337 | 33% helix, 29% strand | P32099 |
| B, D | Glycine cleavage system H protein | protein | 127 | 17% helix, 36% strand | P0A6T9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
- OCT · N-octane · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.79 | 0.81 | 129 | OCT, AMP |
| 2 | 336 | 0.72 | 0.84 | 49 | OCT, AMP |
| 3 | 827 | 0.70 | 0.76 | 84 | empty |
| 4 | 161 | 0.66 | 0.86 | 23 | empty |
| 5 | 172 | 0.58 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 821 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 501 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3A7A · Crystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6T9 · AlphaFold monomer V2.0 prediction for glycine cleavage system H protein (P0A6T9) · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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 0.70
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
- Every structure of UniProt P0A6T9
- Elsewhere: RCSB PDB 3A7A · PDBe 3A7A · UniProt P32099 · UniProt P0A6T9
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