Research workbench
Penicillin-binding protein 2B (pbp-2B) from streptococcus pneumoniae (strain R6)
Analyse Penicillin-binding protein 2B (pbp-2B) from streptococcus pneumoniae (strain R6) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WAF
- Type
- protein
- Length
- 619 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2B
- EC
- 3.4.-.-
- UniProt
- P0A3M6
- Ligands
- CL
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2B (EC 3.4.-.-) | protein | 619 | 35% helix, 22% strand | P0A3M6 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.64 | 0.81 | 48 | empty |
| 2 | 220 | 0.54 | 0.78 | 35 | empty |
| 3 | 85 | 0.32 | 0.73 | 20 | empty |
| 4 | 50 | 0.30 | 0.76 | 16 | empty |
Compared structures
- 2WAF · Penicillin-binding protein 2B (pbp-2B) from streptococcus pneumoniae (strain R6) · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3M6 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2B (P0A3M6) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P0A3M6
- Elsewhere: RCSB PDB 2WAF · PDBe 2WAF · UniProt P0A3M6
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