MolNFT v1 · #56030 · protein
Penicillin-binding protein 2X (PBP2X) from streptococcus pneumoniae
2Z2L: “Penicillin-binding protein 2X (PBP2X) from streptococcus pneumoniae”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.74). MolNFT v1 #56030 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z2L
- Type
- protein
- Length
- 1,277 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2X
- UniProt
- P59676
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2X | protein | 159 | 30% helix, 28% strand | P59676 |
| B, E | Penicillin-binding protein 2X | protein | 367 | 32% helix, 23% strand | P59676 |
| C, F | Penicillin-binding protein 2X | protein | 125 | 17% helix, 30% strand | P59676 |
| D | Penicillin-binding protein 2X | protein | 134 | 22% helix, 26% strand | P59676 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.74 | 0.85 | 42 | empty |
| 2 | 375 | 0.71 | 0.83 | 39 | empty |
| 3 | 690 | 0.68 | 0.76 | 67 | empty |
| 4 | 344 | 0.61 | 0.77 | 51 | empty |
| 5 | 365 | 0.59 | 0.76 | 42 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1789 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 1766 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1500 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1432 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 224 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Z2L · Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae · the same entry in another collection · chain D against D, TM-score 1.00
- P59676 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2X (P59676) · a predicted model of the same protein · chain B 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 P59676
- Elsewhere: RCSB PDB 2Z2L · PDBe 2Z2L · UniProt P59676
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