MolNFT v1 · #152491 · protein
Structure of 3-methylmercaptopropionate CoA ligase mutant K523A in complex with AMP and mmpa
6IJB · AMP-binding domain protein: “Structure of 3-methylmercaptopropionate CoA ligase mutant K523A in complex with AMP and mmpa”. X-ray diffraction, 2 ligands (AMP, A8C), 11 pockets (best druggability 0.80). MolNFT v1 #152491 on…
- PDB
- 6IJB
- Type
- protein
- Length
- 1,071 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMP-binding domain protein
- UniProt
- D0CPY8
- Ligands
- AMP, A8C
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMP-binding domain protein | protein | 533 | 34% helix, 26% strand | D0CPY8 |
| B | AMP-binding domain protein | protein | 538 | 33% helix, 27% strand | D0CPY8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains B
- A8C · 3-(methylsulfanyl)propanoic acid · ligand · chains B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.80 | 0.82 | 98 | AMP, A8C |
| 2 | 214 | 0.59 | 0.81 | 21 | empty |
| 3 | 196 | 0.55 | 0.79 | 21 | empty |
| 4 | 243 | 0.54 | 0.77 | 28 | empty |
| 5 | 188 | 0.49 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 3264 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6IJB · Structure of 3-methylmercaptopropionate CoA ligase mutant K523A in complex with AMP and… · the same entry in another collection · chain A against A, TM-score 1.00
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 D0CPY8
- Elsewhere: RCSB PDB 6IJB · PDBe 6IJB · UniProt D0CPY8
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