Research workbench
PBP2X from streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics
Analyse PBP2X from streptococcus pneumoniae strain 5259 with reduced susceptibility to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RP5
- Type
- protein
- Length
- 1,367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2X
- EC
- 3.4.-.-
- UniProt
- P14677
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2X (EC 3.4.-.-) | protein | 687 | 28% helix, 27% strand | P14677 |
| B | Penicillin-binding protein 2X (EC 3.4.-.-) | protein | 680 | 28% helix, 28% strand | P14677 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.75 | 0.85 | 43 | empty |
| 2 | 528 | 0.73 | 0.82 | 57 | empty |
| 3 | 353 | 0.58 | 0.76 | 40 | SO4 |
| 4 | 392 | 0.57 | 0.75 | 59 | empty |
| 5 | 393 | 0.57 | 0.74 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 800 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1RP5 · PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to… · the same entry in another collection · chain A against A, TM-score 1.00
- P14677 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2X (P14677) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P14677
- Elsewhere: RCSB PDB 1RP5 · PDBe 1RP5 · UniProt P14677
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