MolNFT v1 · #147887 · protein
Tri-functional propionyl-CoA synthase of erythrobacter sp. NAP1 with bound NADP+ and phosphomethylphosphonic acid adenylate ester
6EQO · Acetyl-coenzyme a synthetase: “Tri-functional propionyl-CoA synthase of erythrobacter sp. NAP1 with bound NADP+ and phosphomethylphosphonic…”. X-ray diffraction, 2 ligands (ACP, NAP), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6EQO
- Type
- protein
- Length
- 3,607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-coenzyme a synthetase
- UniProt
- A3WE14
- Ligands
- ACP, NAP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-coenzyme a synthetase | protein | 1804 | 40% helix, 21% strand | A3WE14 |
| B | Acetyl-coenzyme a synthetase | protein | 1803 | 39% helix, 21% strand | A3WE14 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.83 | 0.85 | 91 | NAP |
| 2 | 862 | 0.83 | 0.85 | 93 | NAP |
| 3 | 1123 | 0.83 | 0.84 | 118 | ACP |
| 4 | 1123 | 0.82 | 0.83 | 125 | ACP |
| 5 | 1115 | 0.79 | 0.81 | 127 | empty |
Interfaces
1 interface between chains.
- A–B · 3450 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6EQO · Tri-functional propionyl-CoA synthase of Erythrobacter sp. NAP1 with bound NADP+ and… · the same entry in another collection · chain B against B, 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 A3WE14
- Elsewhere: RCSB PDB 6EQO · PDBe 6EQO · UniProt A3WE14
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