Research workbench
Structural insights into the catalytic mechanism and the role of streptococcus pneumoniae PBP1B
Analyse Structural insights into the catalytic mechanism and the role of streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XD5
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.3.2.-, 2.4.1.129
- UniProt
- Q7CRA4
- Ligands
- S2D, SO4, CL
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.3.2.-, 2.4.1.129) | protein | 469 | 38% helix, 20% strand | Q7CRA4 |
| B | Penicillin-binding protein 1B (EC 2.3.2.-, 2.4.1.129) | protein | 468 | 35% helix, 21% strand | Q7CRA4 |
Ligands and binding sites
- S2D · N-benzoyl-D-alanine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.70 | 0.77 | 81 | S2D, CL |
| 2 | 168 | 0.46 | 0.76 | 29 | SO4 |
| 3 | 131 | 0.42 | 0.75 | 28 | SO4 |
| 4 | 124 | 0.39 | 0.75 | 18 | empty |
| 5 | 126 | 0.39 | 0.74 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XD5 · Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae… · 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 2XD5 · PDBe 2XD5 · UniProt Q7CRA4
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