Research workbench
Cefditoren-acylated penicillin-binding protein 2X (PBP2X) from streptococcus pneumoniae
Analyse Cefditoren-acylated penicillin-binding protein 2X (PBP2X) from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z2M
- Type
- protein
- Length
- 1,234 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2X
- UniProt
- P59676
- Ligands
- CDS, SO4
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2X | protein | 159 | 33% helix, 27% strand | P59676 |
| B | Penicillin-binding protein 2X | protein | 363 | 33% helix, 23% strand | P59676 |
| C, F | Penicillin-binding protein 2X | protein | 125 | 17% helix, 31% strand | P59676 |
| D | Penicillin-binding protein 2X | protein | 100 | 23% helix, 34% strand | P59676 |
| E | Penicillin-binding protein 2X | protein | 362 | 30% helix, 22% strand | P59676 |
Ligands and binding sites
- CDS · (2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-5-[(Z)-2-(4-methyl-1,3-thiazol-5-yl)vinyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains B, E
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.72 | 0.84 | 42 | empty |
| 2 | 395 | 0.72 | 0.83 | 44 | empty |
| 3 | 600 | 0.67 | 0.77 | 56 | empty |
| 4 | 459 | 0.66 | 0.79 | 42 | CDS |
| 5 | 314 | 0.62 | 0.79 | 36 | CDS |
Interfaces
10 interfaces between chains.
- A–B · 1780 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1758 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1462 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1454 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 219 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2Z2M · Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae · the same entry in another collection · chain F against F, TM-score 1.00
- P59676 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2X (P59676) · 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 P59676
- Elsewhere: RCSB PDB 2Z2M · PDBe 2Z2M · UniProt P59676
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