MolNFT v1 · #125472 · protein
Crystal structure of the apc core complex
5L9W · Acetophenone carboxylase delta subunit: “Crystal structure of the apc core complex”. X-ray diffraction, 3 ligands (ADP, HG, K), 20 pockets (best druggability 0.87). MolNFT v1 #125472 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5L9W
- Type
- protein
- Length
- 2,170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetophenone carboxylase delta subunit; Acetophenone carboxylase gamma subunit…
- EC
- 6.4.1.8
- UniProt
- Q5P5G5, Q5P5G4, Q5P5G2, Q5P5G3
- Ligands
- ADP, HG, K
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetophenone carboxylase delta subunit (EC 6.4.1.8) | protein | 683 | 34% helix, 22% strand | Q5P5G5 |
| B | Acetophenone carboxylase gamma subunit (EC 6.4.1.8) | protein | 711 | 36% helix, 26% strand | Q5P5G4 |
| b | Acetophenone carboxylase alpha subunit (EC 6.4.1.8) | protein | 649 | 35% helix, 22% strand | Q5P5G2 |
| C | Acetophenone carboxylase beta subunit (EC 6.4.1.8) | protein | 127 | 13% helix, 32% strand | Q5P5G3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains b
- HG · Mercury (II) ion · metal · 4 copies · chains A, B, C
- K · Potassium ion · metal · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.87 | 0.88 | 157 | HG |
| 2 | 477 | 0.82 | 0.89 | 66 | ADP |
| 3 | 804 | 0.82 | 0.85 | 102 | empty |
| 4 | 397 | 0.77 | 0.86 | 57 | empty |
| 5 | 441 | 0.76 | 0.85 | 61 | EPE |
Interfaces
5 interfaces between chains.
- A–B · 3752 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 3244 Ų buried · 62 hydrogen bonds · protein-protein
- B–b · 2430 Ų buried · 40 hydrogen bonds · protein-protein
- A–b · 147 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 38 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5L9W · Crystal structure of the Apc core complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q5P5G5 · AlphaFold monomer V2.0 prediction for acetophenone carboxylase delta subunit (Q5P5G5) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q5P5G2 · AlphaFold monomer V2.0 prediction for acetophenone carboxylase alpha subunit (Q5P5G2) · a predicted model of the same protein · chain b against A, TM-score 0.98
- Q5P5G3 · AlphaFold monomer V2.0 prediction for acetophenone carboxylase beta subunit (Q5P5G3) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q5P5G4 · AlphaFold monomer V2.0 prediction for acetophenone carboxylase gamma subunit (Q5P5G4) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q5P5G5
- Every structure of UniProt Q5P5G4
- Every structure of UniProt Q5P5G2
- Every structure of UniProt Q5P5G3
- Elsewhere: RCSB PDB 5L9W · PDBe 5L9W · UniProt Q5P5G5 · UniProt Q5P5G4 · UniProt Q5P5G2 · UniProt Q5P5G3
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