MolNFT v1 · #11954 · protein
PBP2X from a highly penicillin-resistant streptococcus pneumoniae clinical isolate
1K25 · Low-affinity penicillin-binding protein 2X: “PBP2X from a highly penicillin-resistant streptococcus pneumoniae clinical isolate”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #11954 on GenesisL1: 3D structure…
- PDB
- 1K25
- Type
- protein
- Length
- 2,237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-affinity penicillin-binding protein 2X
- UniProt
- O34006
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-affinity penicillin-binding protein 2X | protein | 556 | 25% helix, 25% strand | O34006 |
| B | Low-affinity penicillin-binding protein 2X | protein | 575 | 26% helix, 24% strand | O34006 |
| C | Low-affinity penicillin-binding protein 2X | protein | 550 | 24% helix, 22% strand | O34006 |
| D | Low-affinity penicillin-binding protein 2X | protein | 556 | 24% helix, 26% strand | O34006 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.83 | 0.84 | 147 | empty |
| 2 | 852 | 0.79 | 0.82 | 105 | empty |
| 3 | 335 | 0.74 | 0.86 | 42 | empty |
| 4 | 315 | 0.72 | 0.85 | 41 | empty |
| 5 | 441 | 0.71 | 0.82 | 60 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1216 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1190 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1K25 · PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate · 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 O34006
- Elsewhere: RCSB PDB 1K25 · PDBe 1K25 · UniProt O34006
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