Research workbench
A. aeolicus biow with AMP-cpp and pimelate
Analyse A. aeolicus biow with AMP-cpp and pimelate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TV8
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-carboxyhexanoate--CoA ligase
- EC
- 6.2.1.14
- UniProt
- O67575
- Ligands
- APC, PML, MG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-carboxyhexanoate--CoA ligase (EC 6.2.1.14) | protein | 239 | 32% helix, 31% strand | O67575 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- PML · Pimelic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.76 | 0.83 | 49 | APC, MG, PML |
| 2 | 642 | 0.75 | 0.81 | 50 | APC, MG, PML |
| 3 | 126 | 0.43 | 0.76 | 21 | empty |
| 4 | 113 | 0.41 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 O67575
- Elsewhere: RCSB PDB 5TV8 · PDBe 5TV8 · UniProt O67575
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