MolNFT v1 · #53660 · protein
The crystal structure of mature acyl coenzyme A:ISOPENICILLIN N acyltransferase from penicillium chrysogenum
2X1D · Acyl-coenzyme A\:6-aminopenicillanic-acid-acyltransferase…: “The crystal structure of mature acyl coenzyme A:ISOPENICILLIN N acyltransferase from penicillium chrysogenum”. X-ray diffraction, 3 ligands (D1D, CL, PO4), 20 pockets…
- PDB
- 2X1D
- Type
- protein
- Length
- 1,408 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme A\:6-aminopenicillanic-acid-acyltransferase 40 kda form
- EC
- 2.3.1.164
- UniProt
- P15802
- Ligands
- D1D, CL, PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-coenzyme A\:6-aminopenicillanic-acid-acyltransferase 40 kda form (EC 2.3.1.164) | protein | 354 | 38% helix, 25% strand | P15802 |
| B | Acyl-coenzyme A\:6-aminopenicillanic-acid-acyltransferase 40 kda form (EC 2.3.1.164) | protein | 352 | 37% helix, 26% strand | P15802 |
| C | Acyl-coenzyme A\:6-aminopenicillanic-acid-acyltransferase 40 kda form (EC 2.3.1.164) | protein | 351 | 37% helix, 25% strand | P15802 |
| D | Acyl-coenzyme A\:6-aminopenicillanic-acid-acyltransferase 40 kda form (EC 2.3.1.164) | protein | 351 | 37% helix, 26% strand | P15802 |
Ligands and binding sites
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · chains D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, D
- ACT · Acetate ion · additive · 3 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.74 | 0.83 | 42 | empty |
| 2 | 268 | 0.73 | 0.87 | 33 | empty |
| 3 | 283 | 0.71 | 0.85 | 38 | empty |
| 4 | 276 | 0.70 | 0.85 | 38 | empty |
| 5 | 264 | 0.63 | 0.81 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1126 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1054 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 837 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2X1D · 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 2X1D · PDBe 2X1D · UniProt P15802
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