Research workbench
Penicillin-binding protein 2X (pbp 2X) acyl-enzyme complex (biapenem) from streptococcus pneumoniae
Analyse Penicillin-binding protein 2X (pbp 2X) acyl-enzyme complex (biapenem) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZC3
- Type
- protein
- Length
- 1,286 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2X
- UniProt
- P59676
- Ligands
- BMG, SO4
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2X | protein | 158 | 30% helix, 28% strand | P59676 |
| B | Penicillin-binding protein 2X | protein | 366 | 33% helix, 22% strand | P59676 |
| C, F | Penicillin-binding protein 2X | protein | 125 | 17% helix, 30% strand | P59676 |
| D | Penicillin-binding protein 2X | protein | 145 | 28% helix, 26% strand | P59676 |
| E | Penicillin-binding protein 2X | protein | 367 | 31% helix, 22% strand | P59676 |
Ligands and binding sites
- BMG · (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate · ligand · 2 copies · chains B, E
- SO4 · Sulfate ion · ion · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.72 | 0.83 | 43 | empty |
| 2 | 466 | 0.72 | 0.82 | 55 | SO4 |
| 3 | 634 | 0.69 | 0.78 | 65 | empty |
| 4 | 404 | 0.62 | 0.77 | 43 | BMG |
| 5 | 261 | 0.60 | 0.79 | 37 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1751 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1735 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1472 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1445 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 220 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2ZC3 · Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus… · the same entry in another collection · chain E against E, TM-score 1.00
- P59676 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2X (P59676) · a predicted model of the same protein · chain B 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 2ZC3 · PDBe 2ZC3 · UniProt P59676
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