Research workbench
Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (E08)
Analyse Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (E08) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y2M
- Type
- protein
- Length
- 471 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.4.1.129, 2.3.2.-
- UniProt
- Q7CRA4
- Ligands
- E08, NA, CL
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 2.3.2.-) | protein | 471 | 38% helix, 21% strand | Q7CRA4 |
Ligands and binding sites
- E08 · Trihydroxy-[(1S)-1-[(2-propan-2-ylphenyl)carbonylamino]ethyl]boron · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 14 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.53 | 0.75 | 35 | E08, NA |
| 2 | 102 | 0.40 | 0.77 | 23 | CL |
| 3 | 76 | 0.32 | 0.74 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Y2M · Penicillin-binding protein 1B (pbp-1B) in complex with an alkyl boronate (E08) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7CRA4
- Elsewhere: RCSB PDB 2Y2M · PDBe 2Y2M · UniProt Q7CRA4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.