Research workbench
Penicillin-binding protein 1A (pbp-1A) from streptococcus pneumoniae
Analyse Penicillin-binding protein 1A (pbp-1A) from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C6W
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- UniProt
- Q8DR59
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1A | protein | 16 | 0% helix, 50% strand | Q8DR59 |
| B | Penicillin-binding protein 1A | protein | 384 | 33% helix, 19% strand | Q8DR59 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.63 | 0.77 | 46 | CL |
| 2 | 197 | 0.56 | 0.80 | 27 | empty |
| 3 | 125 | 0.41 | 0.75 | 16 | empty |
| 4 | 51 | 0.37 | 0.80 | 12 | empty |
| 5 | 61 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 709 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2C6W · Penicillin-binding protein 1A (pbp-1A) from streptococcus pneumoniae · the same entry in another collection · chain B against B, TM-score 1.00
- Q8DR59 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1A (Q8DR59) · 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 Q8DR59
- Elsewhere: RCSB PDB 2C6W · PDBe 2C6W · UniProt Q8DR59
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