MolNFT v1 · #53661 · protein
The crystal structure of mature acyl coenzyme A:ISOPENICILLIN N acyltransferase from penicillium chrysogenum in complex 6- aminopenicillanic acid
2X1E · Acyl-coenzyme: “The crystal structure of mature acyl coenzyme A:ISOPENICILLIN N acyltransferase from penicillium chrysogenum…”. X-ray diffraction, 3 ligands (X1E, PO4, CL), 18 pockets (best druggability 0.73). MolNFT v1 #53661 on…
- PDB
- 2X1E
- Type
- protein
- Length
- 1,407 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme
- EC
- 2.3.1.164
- UniProt
- P15802
- Ligands
- X1E, PO4, CL
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-coenzyme (EC 2.3.1.164) | protein | 354 | 38% helix, 25% strand | P15802 |
| B | Acyl-coenzyme (EC 2.3.1.164) | protein | 352 | 36% helix, 26% strand | P15802 |
| C | Acyl-coenzyme (EC 2.3.1.164) | protein | 350 | 37% helix, 25% strand | P15802 |
| D | Acyl-coenzyme (EC 2.3.1.164) | protein | 351 | 37% helix, 26% strand | P15802 |
Ligands and binding sites
- X1E · (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.73 | 0.83 | 41 | X1E |
| 2 | 138 | 0.71 | 0.91 | 33 | empty |
| 3 | 355 | 0.70 | 0.83 | 45 | empty |
| 4 | 228 | 0.63 | 0.82 | 27 | empty |
| 5 | 373 | 0.60 | 0.77 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1178 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1111 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 878 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 852 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2X1E · The crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from… · the same entry in another collection · chain D against D, TM-score 1.00
- P15802 · AlphaFold monomer V2.0 prediction for acyl-coenzyme… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P15802
- Elsewhere: RCSB PDB 2X1E · PDBe 2X1E · UniProt P15802
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